Tags: lycosystem/lydata
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Squashed commit of the following: commit b169459417af86048ba8ded5a8b470eb8d3141d8 Author: noemibuehrer <[email protected]> Date: Tue Jul 7 09:13:03 2026 +0200 add KSA citations file commit 67368f14f09bd851d7ad0ffddab996baffd7ee7e Merge: ab677f5 0d28bbf Author: noemibuehrer <[email protected]> Date: Tue Jul 7 08:57:07 2026 +0200 Merge remote-tracking branch 'public/main' into dev commit ab677f57ff495089a83d60c47b4d636873ea8f3b Author: noemibuehrer <[email protected]> Date: Mon Jul 6 15:54:58 2026 +0200 update KSA REAMDE commit 2a2c73901bc94539b50fc797be2b4b70fb970016 Author: noemibuehrer <[email protected]> Date: Mon Jun 8 08:36:52 2026 +0200 shift KSA OC ages randomly commit 933f2d808063652bbfc4a7b3eb1a14791fa25540 Author: noemibuehrer <[email protected]> Date: Thu Jun 4 11:41:36 2026 +0200 shift KSA OC dates randomly commit 73039830fb34de9167409bc46dda1d5ac2890daa Author: noemibuehrer <[email protected]> Date: Thu Jun 4 10:15:15 2026 +0200 remove columns from raw KSA OC file commit 8283cea55c6837c2ff1617f924fb260f5468d170 Author: noemibuehrer <[email protected]> Date: Wed Jun 3 11:20:28 2026 +0200 fix badges for zenodo commit 2f3ed3f651c1b4bab7a8c79fc3dfe9849fc16103 Author: noemibuehrer <[email protected]> Date: Wed Jun 3 10:48:52 2026 +0200 add new info about KSA oral cavity dataset and update README commit 41307ae310efb2e77fce410747591b86c2b9bc25 Merge: 8aca0eb 01a4cf3 Author: noemibuehrer <[email protected]> Date: Tue Jun 2 16:07:18 2026 +0200 Merge branch '2025-ksa-oral-cavity' into dev commit 01a4cf3 Author: noemibuehrer <[email protected]> Date: Tue Jun 2 16:00:59 2026 +0200 update README and fix linting commit 2987467 Merge: e4443f2 475eee8 Author: noemibuehrer <[email protected]> Date: Thu Sep 25 10:56:15 2025 +0200 Merge branch 'dev' into 2025-ksa-oral-cavity
Squashed commit of the following: commit 8aca0eb66246af1c001d19256d98b84c0f31e1c8 Author: Roman Ludwig <[email protected]> Date: Wed Sep 24 11:40:24 2025 +0200 add info about squash commits commit 475eee8 Author: Roman Ludwig <[email protected]> Date: Mon Sep 22 12:27:28 2025 +0200 shift UKF dates randomly commit a4499ab Author: Roman Ludwig <[email protected]> Date: Mon Sep 22 12:22:56 2025 +0200 shift UMCG dates randomly commit c79a327 Author: Roman Ludwig <[email protected]> Date: Fri Sep 5 10:56:39 2025 +0200 remove follow-up & recurrence from UMCG data commit 90c4fce Author: Roman Ludwig <[email protected]> Date: Fri Sep 5 10:51:10 2025 +0200 remove follop-up & recurrence from UKF data commit 1909c71 Merge: 1e28727 4eb6177 Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 15:25:17 2025 +0200 Merge branch 'timeline-plot' into dev commit 4eb6177 Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 15:24:49 2025 +0200 add timeline over patients against diagnosis times commit 78b2b2f Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 14:27:16 2025 +0200 fix UMCG diagnose date in 1800 to 2018 commit d734461 Author: Roman Ludwig <[email protected]> Date: Tue Sep 2 16:41:08 2025 +0200 start working on a timeline plot commit 1e28727 Author: Roman Ludwig <[email protected]> Date: Mon Sep 1 15:22:36 2025 +0200 add UKF subsite/T-cat. area plot again commit 35c06b8 Author: Roman Ludwig <[email protected]> Date: Wed Aug 27 12:23:40 2025 +0200 add preliminary zenodo DOIs commit 3de6172 Author: Roman Ludwig <[email protected]> Date: Wed Aug 27 12:22:31 2025 +0200 change which figures to plot for new data commit bba51f3 Author: Roman Ludwig <[email protected]> Date: Tue Aug 26 10:22:18 2025 +0200 markdownlint fix jinja templates commit bcc47e4 Author: Roman Ludwig <[email protected]> Date: Tue Aug 26 10:20:22 2025 +0200 fix some typos commit 5c219f5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 13:50:14 2025 +0200 all datasets (except UMCG) cast & valid commit 8375751 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 12:27:43 2025 +0200 2023 CLB passes validation commit 0e624c4 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 12:04:40 2025 +0200 2025 USZ passes validation commit 1144d65 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:32:05 2025 +0200 cast every dataset to cleaner dtype commit 62d96c6 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:08:52 2025 +0200 fix date 12/11/!2 to 12/11/2012 in HVH data commit 32a17f9 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:03:44 2025 +0200 change 5011 to 2011 in ISB data commit b085dfa Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 14:36:13 2025 +0200 rename `stage_prefix` to `t_stage_prefix` & MX=-1 commit e68141f Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 17:41:33 2025 +0200 remove MX (-1), as it is not valid TNM stage commit ddd65ea Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 11:05:57 2025 +0200 rename `dist_mid` to `dist_to_midline` commit fc7c60d Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 09:55:37 2025 +0200 rm ukf.docx commit 292628a Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 14:30:04 2025 +0200 rm empty UKF cols & document follo-up/recurrence commit 0c3b448 Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 14:14:56 2025 +0200 add metainfor to UKF dataset commit c1be95a Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 12:55:35 2025 +0200 shift 2025-USZ dates randomly commit ad0ab7b Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 10:44:20 2025 +0200 fix location of two 2025 USZ patients commit de48e8a Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 17:02:07 2025 +0200 add hypo/larynx are plots to figures folders commit 8ca7503 Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 15:50:08 2025 +0200 add (unused) script to infer location from ICD commit c11011a Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 11:28:55 2025 +0200 fine-tune area plot commit af0016d Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 17:15:03 2025 +0200 make first version of subsite/T-stage plot commit 66daff5 Merge: ab04379 ea9d4b5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 13:55:43 2025 +0200 Merge branch '23-unique-ids' into dev commit ea9d4b5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 13:22:45 2025 +0200 add N-stage suffix to 2025-usz Also, for some patients typos were corrected. Thus, one more patient is now in the table because their ICD code was corrected. commit 6c56a63 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 17:38:56 2025 +0200 don't use -1 for MX stage, but simply `None` commit 4b519c6 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 14:09:34 2025 +0200 add unique IDs to every row Fixes: #23 commit c5993c1 Merge: ab04379 f622116 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 10:04:42 2025 +0200 Merge branch '21-change-2nd-level-headers' into dev commit f622116 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 10:00:05 2025 +0200 make every cmd use its own set of dependencies commit 08fd2bc Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 09:33:34 2025 +0200 change docs about midlvl cols to "core" commit fb55afa Author: Roman Ludwig <[email protected]> Date: Thu Jul 31 14:44:51 2025 +0200 start changing midlvl cols to "core" Some scripts aren't working yet, though. Related: #21 commit 099f4e3 Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 16:33:11 2025 +0200 add info on UKF data & reproducing pipeline commit 83654ae Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 16:14:04 2025 +0200 make scripts' deps independent using uv commit 5a96af5 Merge: c44bef4 b0456ba Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 15:08:29 2025 +0200 pin numpy dependency commit b0456ba Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 15:02:55 2025 +0200 pin numpy dependency commit c44bef4 Author: Roman Ludwig <[email protected]> Date: Fri Jul 25 11:14:06 2025 +0200 update/improve UMCG/USZ column description commit d3b511b Author: Roman Ludwig <[email protected]> Date: Wed Jul 23 08:51:45 2025 +0200 update & refactor scripts, rerun pipeline commit 894cbe1 Author: Roman Ludwig <[email protected]> Date: Tue Jul 22 17:22:36 2025 +0200 update scripts & rerun with new lyscripts commit ce2ac25 Author: Roman Ludwig <[email protected]> Date: Tue Jul 22 11:31:55 2025 +0200 rerun pipeline (figures not yet working) commit 25d04f7 Author: Roman Ludwig <[email protected]> Date: Mon Jul 21 16:43:32 2025 +0200 replace `#` and `1` with `info` in 2nd lvl headers commit ab04379 Author: Roman Ludwig <[email protected]> Date: Mon Jul 21 13:42:07 2025 +0200 generate figures for 2025-usz-... too commit fe439c2 Merge: 325b469 fbf73af Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 14:08:42 2025 +0200 merge: branch '2025-usz-hypopharynx-larynx' into 'dev' commit 325b469 Merge: 819d83f a98137c Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 13:32:54 2025 +0200 merge: branch '2025-umcg-hypopharynx-larynx' into 'dev' commit fbf73af Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 11:37:41 2025 +0200 add/update README(s) commit 8015cf3 Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 10:40:50 2025 +0200 add/update CITATION.cff commit 60a4723 Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 10:38:00 2025 +0200 add CITATION.cff validation as pre-commit hooks commit c2eca36 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 11:24:24 2025 +0200 add IDs to table and make pipeline work again commit a98137c Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:24:31 2025 +0200 add citations file to UMCG dataset commit 819d83f Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:15:41 2025 +0200 Revert "move licenses" This reverts commit f7a6ae3. commit f7a6ae3 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:15:01 2025 +0200 move licenses commit 61e456d Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:13:57 2025 +0200 improve legal framework commit 5b36333 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 09:48:30 2025 +0200 small fix in readme templates commit 7fd4c65 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 09:30:34 2025 +0200 update readme & reorder pipeline commit 6da1d4e Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 15:57:00 2025 +0200 refactor scripts and update DVC configuration - update DVC to use latest lyscripts - update UMCG to new file path under 2025-... - remove unnecessary stages - add rendering of UMCG data README - refactor Python scripts commit fa163cb Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 15:40:13 2025 +0200 stop tracking 2025-umcg-hypopharynx-larynx/README.md commit 2c94f73 Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 13:56:24 2025 +0200 rename hypopharynx-larynx USZ data to 2025 commit 60651e6 Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 12:50:50 2025 +0200 rename UMCG data to 2025 commit c15b908 Author: Roman Ludwig <[email protected]> Date: Tue Jul 8 18:28:44 2025 +0200 add contributing guide Related: #22 commit 60cc9f0 Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 15:03:36 2025 +0200 reduce unnecessary pipeline steps & rerun commit 0b03802 Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 15:00:51 2025 +0200 recompile Python requirements & rerun pipeline commit 5049dad Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 14:57:05 2025 +0200 remove library and related files/config The library now lives in its own dedicated repo and there is no need anymore to track it here. Fixes: #20 commit d8cdb38 Author: Roman Ludwig <[email protected]> Date: Tue Jun 24 16:03:25 2025 +0200 fix: broken lyscripts docs links commit 340753e Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 14:46:37 2025 +0200 chore: update links after transfer to lycosystem commit 5876fd2 Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 13:41:41 2025 +0200 ci: rename README.template to README.md.jinja commit 85a28f0 Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 11:36:41 2025 +0200 chore: update pre-commit & ruff rules commit abc9236 Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:53:43 2025 +0100 fix missing age in last patient commit c2e87a0 Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:50:40 2025 +0100 fix missing subsite in one patient This particular patient was double checked with the people from Freiburg. commit 2f9b6fb Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:48:37 2025 +0100 add missing M0 stage for two patients commit bab314e Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:25:40 2025 +0100 add 'c' prefix to T-stage All patients where at least clinically staged, so they must all have at least a 'c' as T-stage prefix. commit 61ad709 Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 11:48:36 2025 +0100 add conflicts to pipeline commit bf0a1cd Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 11:48:14 2025 +0100 add script to plot conflicts btw modalities commit 467e856 Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 09:43:51 2025 +0100 rename `FNA` to `sonography` In a call with Dr. Rühle, he mentioned that they used `FNA` to encode a sonography diagnosis. So, we renamed that. commit 15ff90e Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:29:07 2025 +0100 remove another weird quote string commit cb605d4 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:26:32 2025 +0100 replace id with institution name commit 3841e8e Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:02:28 2025 +0100 reorder & add id nums to data.csv I applied the following commands in order: ```bash lyscripts data join --inputs ruehle.csv schaefer.csv --output joined.csv nl -b p'^,' joined.csv > numbered.csv sed 's/^[[:space:]]*\([0-9]*\)[[:space:]]*/\1/' numbered.csv > data.csv ``` commit c8de9a1 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 13:48:28 2025 +0100 concat & add id nums to ruehle & schaefer commit 9eecdfb Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:41:17 2025 +0100 make central true if position is central commit 5df4944 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:39:21 2025 +0100 remove weird string of quotes from schafer.csv commit 1db3aa8 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:37:54 2025 +0100 fix T-stage prefix and 'ambiguous' position commit 0daa185 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:34:39 2025 +0100 fix negative age in one patient commit ce4ee5b Author: Roman Ludwig <[email protected]> Date: Wed Jan 15 17:09:15 2025 +0100 add parsed CSV files from Freiburg (UKF) commit 3412f8e Author: Roman Ludwig <[email protected]> Date: Thu Apr 4 09:54:42 2024 +0200 rerun pipeline (no changes?) commit 0fb37bf Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 12:24:07 2024 +0200 add follow-up & recurrene info commit 167e6e0 Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 11:26:03 2024 +0200 fix wrong regional recurrence in one patient commit 9d95484 Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 11:00:20 2024 +0200 add distance to midline commit 63c9d1b Author: Roman Ludwig <[email protected]> Date: Mon Mar 25 16:51:21 2024 +0100 rerun pipeline commit 91fd97f Author: Roman Ludwig <[email protected]> Date: Mon Mar 25 16:45:46 2024 +0100 del C10.8 patient & change C12.9 to C12 commit 093a1a4 Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 15:22:15 2024 +0100 fix smoking & T-cat, create plots commit ff5d4ea Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 14:52:18 2024 +0100 join surgery & radiotherapy data commit b12fc36 Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 14:38:34 2024 +0100 add LNL VII to surgery patients commit 66147fc Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:49:04 2024 +0100 rerun after merge commit af74a3a Merge: a4b4210 258ce1a Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:47:55 2024 +0100 Merge branch 'tmp' into 2024-umcg-hypopharynx-larynx commit 258ce1a Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:47:17 2024 +0100 join UMCG datasets & rerun pipeline commit a4b4210 Author: rmnldwg <[email protected]> Date: Wed Feb 21 14:22:02 2024 +0100 add LNL VII to radiotherapy patients commit 52a35f5 Author: Roman Ludwig <[email protected]> Date: Tue Feb 20 09:56:55 2024 +0100 create first version of mapping of surgical data commit 56bd28a Author: rmnldwg <[email protected]> Date: Wed Feb 14 17:33:03 2024 +0100 choose earliest of dates & set unknown age to -1 commit eadff41 Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:30:22 2024 +0100 fix all True involvement commit b723519 Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:16:16 2024 +0100 fix mixxing age commit 710a34a Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:12:20 2024 +0100 add lower bound to lyscripts commit 24983ad Author: rmnldwg <[email protected]> Date: Wed Feb 14 14:50:39 2024 +0100 first successful tranformation of rad data commit c036695 Author: Roman Ludwig <[email protected]> Date: Wed Feb 14 10:46:51 2024 +0100 start writing mapping for UMCG dataset commit caecfc6 Author: Roman Ludwig <[email protected]> Date: Tue Feb 13 13:53:17 2024 +0100 update midline extension info in radiotherapy data commit b657af1 Author: rmnldwg <[email protected]> Date: Mon Feb 12 17:32:04 2024 +0100 add raw data from UMCG commit 843a895 Author: rmnldwg <[email protected]> Date: Tue Nov 21 11:06:32 2023 +0100 add id, insititution to hypo/larynx data via stage commit 23098ee Merge: c407abd 304d985 Author: rmnldwg <[email protected]> Date: Tue Nov 21 11:05:04 2023 +0100 merge: branch 'main' into '2023-usz-hypopharynx-larynx' commit c407abd Merge: 0cd41e4 29221aa Author: rmnldwg <[email protected]> Date: Tue Nov 21 09:38:52 2023 +0100 merge: branch 'main' into '2023-usz-hypopharynx-larynx' commit 0cd41e4 Author: rmnldwg <[email protected]> Date: Fri Oct 20 12:59:49 2023 +0800 fix pCT date & add consensus to patients commit 5c3d19a Author: rmnldwg <[email protected]> Date: Fri Oct 20 11:53:25 2023 +0800 create data.csv from raw parsed.csv commit 7b97ac8 Author: rmnldwg <[email protected]> Date: Thu Oct 19 13:36:20 2023 +0800 change "ambiguous" to "central" in tumor side commit 6e2575d Author: rmnldwg <[email protected]> Date: Tue Oct 17 16:20:15 2023 +0800 add parsed CSV data table
Squashed commit of the following: commit 8aca0eb66246af1c001d19256d98b84c0f31e1c8 Author: Roman Ludwig <[email protected]> Date: Wed Sep 24 11:40:24 2025 +0200 add info about squash commits commit 475eee8 Author: Roman Ludwig <[email protected]> Date: Mon Sep 22 12:27:28 2025 +0200 shift UKF dates randomly commit a4499ab Author: Roman Ludwig <[email protected]> Date: Mon Sep 22 12:22:56 2025 +0200 shift UMCG dates randomly commit c79a327 Author: Roman Ludwig <[email protected]> Date: Fri Sep 5 10:56:39 2025 +0200 remove follow-up & recurrence from UMCG data commit 90c4fce Author: Roman Ludwig <[email protected]> Date: Fri Sep 5 10:51:10 2025 +0200 remove follop-up & recurrence from UKF data commit 1909c71 Merge: 1e28727 4eb6177 Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 15:25:17 2025 +0200 Merge branch 'timeline-plot' into dev commit 4eb6177 Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 15:24:49 2025 +0200 add timeline over patients against diagnosis times commit 78b2b2f Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 14:27:16 2025 +0200 fix UMCG diagnose date in 1800 to 2018 commit d734461 Author: Roman Ludwig <[email protected]> Date: Tue Sep 2 16:41:08 2025 +0200 start working on a timeline plot commit 1e28727 Author: Roman Ludwig <[email protected]> Date: Mon Sep 1 15:22:36 2025 +0200 add UKF subsite/T-cat. area plot again commit 35c06b8 Author: Roman Ludwig <[email protected]> Date: Wed Aug 27 12:23:40 2025 +0200 add preliminary zenodo DOIs commit 3de6172 Author: Roman Ludwig <[email protected]> Date: Wed Aug 27 12:22:31 2025 +0200 change which figures to plot for new data commit bba51f3 Author: Roman Ludwig <[email protected]> Date: Tue Aug 26 10:22:18 2025 +0200 markdownlint fix jinja templates commit bcc47e4 Author: Roman Ludwig <[email protected]> Date: Tue Aug 26 10:20:22 2025 +0200 fix some typos commit 5c219f5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 13:50:14 2025 +0200 all datasets (except UMCG) cast & valid commit 8375751 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 12:27:43 2025 +0200 2023 CLB passes validation commit 0e624c4 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 12:04:40 2025 +0200 2025 USZ passes validation commit 1144d65 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:32:05 2025 +0200 cast every dataset to cleaner dtype commit 62d96c6 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:08:52 2025 +0200 fix date 12/11/!2 to 12/11/2012 in HVH data commit 32a17f9 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:03:44 2025 +0200 change 5011 to 2011 in ISB data commit b085dfa Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 14:36:13 2025 +0200 rename `stage_prefix` to `t_stage_prefix` & MX=-1 commit e68141f Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 17:41:33 2025 +0200 remove MX (-1), as it is not valid TNM stage commit ddd65ea Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 11:05:57 2025 +0200 rename `dist_mid` to `dist_to_midline` commit fc7c60d Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 09:55:37 2025 +0200 rm ukf.docx commit 292628a Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 14:30:04 2025 +0200 rm empty UKF cols & document follo-up/recurrence commit 0c3b448 Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 14:14:56 2025 +0200 add metainfor to UKF dataset commit c1be95a Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 12:55:35 2025 +0200 shift 2025-USZ dates randomly commit ad0ab7b Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 10:44:20 2025 +0200 fix location of two 2025 USZ patients commit de48e8a Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 17:02:07 2025 +0200 add hypo/larynx are plots to figures folders commit 8ca7503 Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 15:50:08 2025 +0200 add (unused) script to infer location from ICD commit c11011a Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 11:28:55 2025 +0200 fine-tune area plot commit af0016d Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 17:15:03 2025 +0200 make first version of subsite/T-stage plot commit 66daff5 Merge: ab04379 ea9d4b5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 13:55:43 2025 +0200 Merge branch '23-unique-ids' into dev commit ea9d4b5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 13:22:45 2025 +0200 add N-stage suffix to 2025-usz Also, for some patients typos were corrected. Thus, one more patient is now in the table because their ICD code was corrected. commit 6c56a63 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 17:38:56 2025 +0200 don't use -1 for MX stage, but simply `None` commit 4b519c6 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 14:09:34 2025 +0200 add unique IDs to every row Fixes: #23 commit c5993c1 Merge: ab04379 f622116 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 10:04:42 2025 +0200 Merge branch '21-change-2nd-level-headers' into dev commit f622116 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 10:00:05 2025 +0200 make every cmd use its own set of dependencies commit 08fd2bc Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 09:33:34 2025 +0200 change docs about midlvl cols to "core" commit fb55afa Author: Roman Ludwig <[email protected]> Date: Thu Jul 31 14:44:51 2025 +0200 start changing midlvl cols to "core" Some scripts aren't working yet, though. Related: #21 commit 099f4e3 Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 16:33:11 2025 +0200 add info on UKF data & reproducing pipeline commit 83654ae Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 16:14:04 2025 +0200 make scripts' deps independent using uv commit 5a96af5 Merge: c44bef4 b0456ba Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 15:08:29 2025 +0200 pin numpy dependency commit b0456ba Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 15:02:55 2025 +0200 pin numpy dependency commit c44bef4 Author: Roman Ludwig <[email protected]> Date: Fri Jul 25 11:14:06 2025 +0200 update/improve UMCG/USZ column description commit d3b511b Author: Roman Ludwig <[email protected]> Date: Wed Jul 23 08:51:45 2025 +0200 update & refactor scripts, rerun pipeline commit 894cbe1 Author: Roman Ludwig <[email protected]> Date: Tue Jul 22 17:22:36 2025 +0200 update scripts & rerun with new lyscripts commit ce2ac25 Author: Roman Ludwig <[email protected]> Date: Tue Jul 22 11:31:55 2025 +0200 rerun pipeline (figures not yet working) commit 25d04f7 Author: Roman Ludwig <[email protected]> Date: Mon Jul 21 16:43:32 2025 +0200 replace `#` and `1` with `info` in 2nd lvl headers commit ab04379 Author: Roman Ludwig <[email protected]> Date: Mon Jul 21 13:42:07 2025 +0200 generate figures for 2025-usz-... too commit fe439c2 Merge: 325b469 fbf73af Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 14:08:42 2025 +0200 merge: branch '2025-usz-hypopharynx-larynx' into 'dev' commit 325b469 Merge: 819d83f a98137c Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 13:32:54 2025 +0200 merge: branch '2025-umcg-hypopharynx-larynx' into 'dev' commit fbf73af Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 11:37:41 2025 +0200 add/update README(s) commit 8015cf3 Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 10:40:50 2025 +0200 add/update CITATION.cff commit 60a4723 Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 10:38:00 2025 +0200 add CITATION.cff validation as pre-commit hooks commit c2eca36 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 11:24:24 2025 +0200 add IDs to table and make pipeline work again commit a98137c Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:24:31 2025 +0200 add citations file to UMCG dataset commit 819d83f Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:15:41 2025 +0200 Revert "move licenses" This reverts commit f7a6ae3. commit f7a6ae3 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:15:01 2025 +0200 move licenses commit 61e456d Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:13:57 2025 +0200 improve legal framework commit 5b36333 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 09:48:30 2025 +0200 small fix in readme templates commit 7fd4c65 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 09:30:34 2025 +0200 update readme & reorder pipeline commit 6da1d4e Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 15:57:00 2025 +0200 refactor scripts and update DVC configuration - update DVC to use latest lyscripts - update UMCG to new file path under 2025-... - remove unnecessary stages - add rendering of UMCG data README - refactor Python scripts commit fa163cb Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 15:40:13 2025 +0200 stop tracking 2025-umcg-hypopharynx-larynx/README.md commit 2c94f73 Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 13:56:24 2025 +0200 rename hypopharynx-larynx USZ data to 2025 commit 60651e6 Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 12:50:50 2025 +0200 rename UMCG data to 2025 commit c15b908 Author: Roman Ludwig <[email protected]> Date: Tue Jul 8 18:28:44 2025 +0200 add contributing guide Related: #22 commit 60cc9f0 Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 15:03:36 2025 +0200 reduce unnecessary pipeline steps & rerun commit 0b03802 Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 15:00:51 2025 +0200 recompile Python requirements & rerun pipeline commit 5049dad Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 14:57:05 2025 +0200 remove library and related files/config The library now lives in its own dedicated repo and there is no need anymore to track it here. Fixes: #20 commit d8cdb38 Author: Roman Ludwig <[email protected]> Date: Tue Jun 24 16:03:25 2025 +0200 fix: broken lyscripts docs links commit 340753e Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 14:46:37 2025 +0200 chore: update links after transfer to lycosystem commit 5876fd2 Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 13:41:41 2025 +0200 ci: rename README.template to README.md.jinja commit 85a28f0 Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 11:36:41 2025 +0200 chore: update pre-commit & ruff rules commit abc9236 Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:53:43 2025 +0100 fix missing age in last patient commit c2e87a0 Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:50:40 2025 +0100 fix missing subsite in one patient This particular patient was double checked with the people from Freiburg. commit 2f9b6fb Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:48:37 2025 +0100 add missing M0 stage for two patients commit bab314e Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:25:40 2025 +0100 add 'c' prefix to T-stage All patients where at least clinically staged, so they must all have at least a 'c' as T-stage prefix. commit 61ad709 Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 11:48:36 2025 +0100 add conflicts to pipeline commit bf0a1cd Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 11:48:14 2025 +0100 add script to plot conflicts btw modalities commit 467e856 Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 09:43:51 2025 +0100 rename `FNA` to `sonography` In a call with Dr. Rühle, he mentioned that they used `FNA` to encode a sonography diagnosis. So, we renamed that. commit 15ff90e Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:29:07 2025 +0100 remove another weird quote string commit cb605d4 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:26:32 2025 +0100 replace id with institution name commit 3841e8e Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:02:28 2025 +0100 reorder & add id nums to data.csv I applied the following commands in order: ```bash lyscripts data join --inputs ruehle.csv schaefer.csv --output joined.csv nl -b p'^,' joined.csv > numbered.csv sed 's/^[[:space:]]*\([0-9]*\)[[:space:]]*/\1/' numbered.csv > data.csv ``` commit c8de9a1 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 13:48:28 2025 +0100 concat & add id nums to ruehle & schaefer commit 9eecdfb Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:41:17 2025 +0100 make central true if position is central commit 5df4944 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:39:21 2025 +0100 remove weird string of quotes from schafer.csv commit 1db3aa8 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:37:54 2025 +0100 fix T-stage prefix and 'ambiguous' position commit 0daa185 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:34:39 2025 +0100 fix negative age in one patient commit ce4ee5b Author: Roman Ludwig <[email protected]> Date: Wed Jan 15 17:09:15 2025 +0100 add parsed CSV files from Freiburg (UKF) commit 3412f8e Author: Roman Ludwig <[email protected]> Date: Thu Apr 4 09:54:42 2024 +0200 rerun pipeline (no changes?) commit 0fb37bf Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 12:24:07 2024 +0200 add follow-up & recurrene info commit 167e6e0 Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 11:26:03 2024 +0200 fix wrong regional recurrence in one patient commit 9d95484 Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 11:00:20 2024 +0200 add distance to midline commit 63c9d1b Author: Roman Ludwig <[email protected]> Date: Mon Mar 25 16:51:21 2024 +0100 rerun pipeline commit 91fd97f Author: Roman Ludwig <[email protected]> Date: Mon Mar 25 16:45:46 2024 +0100 del C10.8 patient & change C12.9 to C12 commit 093a1a4 Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 15:22:15 2024 +0100 fix smoking & T-cat, create plots commit ff5d4ea Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 14:52:18 2024 +0100 join surgery & radiotherapy data commit b12fc36 Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 14:38:34 2024 +0100 add LNL VII to surgery patients commit 66147fc Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:49:04 2024 +0100 rerun after merge commit af74a3a Merge: a4b4210 258ce1a Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:47:55 2024 +0100 Merge branch 'tmp' into 2024-umcg-hypopharynx-larynx commit 258ce1a Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:47:17 2024 +0100 join UMCG datasets & rerun pipeline commit a4b4210 Author: rmnldwg <[email protected]> Date: Wed Feb 21 14:22:02 2024 +0100 add LNL VII to radiotherapy patients commit 52a35f5 Author: Roman Ludwig <[email protected]> Date: Tue Feb 20 09:56:55 2024 +0100 create first version of mapping of surgical data commit 56bd28a Author: rmnldwg <[email protected]> Date: Wed Feb 14 17:33:03 2024 +0100 choose earliest of dates & set unknown age to -1 commit eadff41 Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:30:22 2024 +0100 fix all True involvement commit b723519 Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:16:16 2024 +0100 fix mixxing age commit 710a34a Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:12:20 2024 +0100 add lower bound to lyscripts commit 24983ad Author: rmnldwg <[email protected]> Date: Wed Feb 14 14:50:39 2024 +0100 first successful tranformation of rad data commit c036695 Author: Roman Ludwig <[email protected]> Date: Wed Feb 14 10:46:51 2024 +0100 start writing mapping for UMCG dataset commit caecfc6 Author: Roman Ludwig <[email protected]> Date: Tue Feb 13 13:53:17 2024 +0100 update midline extension info in radiotherapy data commit b657af1 Author: rmnldwg <[email protected]> Date: Mon Feb 12 17:32:04 2024 +0100 add raw data from UMCG commit 843a895 Author: rmnldwg <[email protected]> Date: Tue Nov 21 11:06:32 2023 +0100 add id, insititution to hypo/larynx data via stage commit 23098ee Merge: c407abd 304d985 Author: rmnldwg <[email protected]> Date: Tue Nov 21 11:05:04 2023 +0100 merge: branch 'main' into '2023-usz-hypopharynx-larynx' commit c407abd Merge: 0cd41e4 29221aa Author: rmnldwg <[email protected]> Date: Tue Nov 21 09:38:52 2023 +0100 merge: branch 'main' into '2023-usz-hypopharynx-larynx' commit 0cd41e4 Author: rmnldwg <[email protected]> Date: Fri Oct 20 12:59:49 2023 +0800 fix pCT date & add consensus to patients commit 5c3d19a Author: rmnldwg <[email protected]> Date: Fri Oct 20 11:53:25 2023 +0800 create data.csv from raw parsed.csv commit 7b97ac8 Author: rmnldwg <[email protected]> Date: Thu Oct 19 13:36:20 2023 +0800 change "ambiguous" to "central" in tumor side commit 6e2575d Author: rmnldwg <[email protected]> Date: Tue Oct 17 16:20:15 2023 +0800 add parsed CSV data table
Squashed commit of the following: commit 8aca0eb66246af1c001d19256d98b84c0f31e1c8 Author: Roman Ludwig <[email protected]> Date: Wed Sep 24 11:40:24 2025 +0200 add info about squash commits commit 475eee8 Author: Roman Ludwig <[email protected]> Date: Mon Sep 22 12:27:28 2025 +0200 shift UKF dates randomly commit a4499ab Author: Roman Ludwig <[email protected]> Date: Mon Sep 22 12:22:56 2025 +0200 shift UMCG dates randomly commit c79a327 Author: Roman Ludwig <[email protected]> Date: Fri Sep 5 10:56:39 2025 +0200 remove follow-up & recurrence from UMCG data commit 90c4fce Author: Roman Ludwig <[email protected]> Date: Fri Sep 5 10:51:10 2025 +0200 remove follop-up & recurrence from UKF data commit 1909c71 Merge: 1e28727 4eb6177 Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 15:25:17 2025 +0200 Merge branch 'timeline-plot' into dev commit 4eb6177 Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 15:24:49 2025 +0200 add timeline over patients against diagnosis times commit 78b2b2f Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 14:27:16 2025 +0200 fix UMCG diagnose date in 1800 to 2018 commit d734461 Author: Roman Ludwig <[email protected]> Date: Tue Sep 2 16:41:08 2025 +0200 start working on a timeline plot commit 1e28727 Author: Roman Ludwig <[email protected]> Date: Mon Sep 1 15:22:36 2025 +0200 add UKF subsite/T-cat. area plot again commit 35c06b8 Author: Roman Ludwig <[email protected]> Date: Wed Aug 27 12:23:40 2025 +0200 add preliminary zenodo DOIs commit 3de6172 Author: Roman Ludwig <[email protected]> Date: Wed Aug 27 12:22:31 2025 +0200 change which figures to plot for new data commit bba51f3 Author: Roman Ludwig <[email protected]> Date: Tue Aug 26 10:22:18 2025 +0200 markdownlint fix jinja templates commit bcc47e4 Author: Roman Ludwig <[email protected]> Date: Tue Aug 26 10:20:22 2025 +0200 fix some typos commit 5c219f5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 13:50:14 2025 +0200 all datasets (except UMCG) cast & valid commit 8375751 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 12:27:43 2025 +0200 2023 CLB passes validation commit 0e624c4 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 12:04:40 2025 +0200 2025 USZ passes validation commit 1144d65 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:32:05 2025 +0200 cast every dataset to cleaner dtype commit 62d96c6 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:08:52 2025 +0200 fix date 12/11/!2 to 12/11/2012 in HVH data commit 32a17f9 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:03:44 2025 +0200 change 5011 to 2011 in ISB data commit b085dfa Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 14:36:13 2025 +0200 rename `stage_prefix` to `t_stage_prefix` & MX=-1 commit e68141f Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 17:41:33 2025 +0200 remove MX (-1), as it is not valid TNM stage commit ddd65ea Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 11:05:57 2025 +0200 rename `dist_mid` to `dist_to_midline` commit fc7c60d Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 09:55:37 2025 +0200 rm ukf.docx commit 292628a Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 14:30:04 2025 +0200 rm empty UKF cols & document follo-up/recurrence commit 0c3b448 Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 14:14:56 2025 +0200 add metainfor to UKF dataset commit c1be95a Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 12:55:35 2025 +0200 shift 2025-USZ dates randomly commit ad0ab7b Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 10:44:20 2025 +0200 fix location of two 2025 USZ patients commit de48e8a Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 17:02:07 2025 +0200 add hypo/larynx are plots to figures folders commit 8ca7503 Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 15:50:08 2025 +0200 add (unused) script to infer location from ICD commit c11011a Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 11:28:55 2025 +0200 fine-tune area plot commit af0016d Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 17:15:03 2025 +0200 make first version of subsite/T-stage plot commit 66daff5 Merge: ab04379 ea9d4b5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 13:55:43 2025 +0200 Merge branch '23-unique-ids' into dev commit ea9d4b5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 13:22:45 2025 +0200 add N-stage suffix to 2025-usz Also, for some patients typos were corrected. Thus, one more patient is now in the table because their ICD code was corrected. commit 6c56a63 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 17:38:56 2025 +0200 don't use -1 for MX stage, but simply `None` commit 4b519c6 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 14:09:34 2025 +0200 add unique IDs to every row Fixes: #23 commit c5993c1 Merge: ab04379 f622116 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 10:04:42 2025 +0200 Merge branch '21-change-2nd-level-headers' into dev commit f622116 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 10:00:05 2025 +0200 make every cmd use its own set of dependencies commit 08fd2bc Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 09:33:34 2025 +0200 change docs about midlvl cols to "core" commit fb55afa Author: Roman Ludwig <[email protected]> Date: Thu Jul 31 14:44:51 2025 +0200 start changing midlvl cols to "core" Some scripts aren't working yet, though. Related: #21 commit 099f4e3 Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 16:33:11 2025 +0200 add info on UKF data & reproducing pipeline commit 83654ae Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 16:14:04 2025 +0200 make scripts' deps independent using uv commit 5a96af5 Merge: c44bef4 b0456ba Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 15:08:29 2025 +0200 pin numpy dependency commit b0456ba Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 15:02:55 2025 +0200 pin numpy dependency commit c44bef4 Author: Roman Ludwig <[email protected]> Date: Fri Jul 25 11:14:06 2025 +0200 update/improve UMCG/USZ column description commit d3b511b Author: Roman Ludwig <[email protected]> Date: Wed Jul 23 08:51:45 2025 +0200 update & refactor scripts, rerun pipeline commit 894cbe1 Author: Roman Ludwig <[email protected]> Date: Tue Jul 22 17:22:36 2025 +0200 update scripts & rerun with new lyscripts commit ce2ac25 Author: Roman Ludwig <[email protected]> Date: Tue Jul 22 11:31:55 2025 +0200 rerun pipeline (figures not yet working) commit 25d04f7 Author: Roman Ludwig <[email protected]> Date: Mon Jul 21 16:43:32 2025 +0200 replace `#` and `1` with `info` in 2nd lvl headers commit ab04379 Author: Roman Ludwig <[email protected]> Date: Mon Jul 21 13:42:07 2025 +0200 generate figures for 2025-usz-... too commit fe439c2 Merge: 325b469 fbf73af Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 14:08:42 2025 +0200 merge: branch '2025-usz-hypopharynx-larynx' into 'dev' commit 325b469 Merge: 819d83f a98137c Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 13:32:54 2025 +0200 merge: branch '2025-umcg-hypopharynx-larynx' into 'dev' commit fbf73af Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 11:37:41 2025 +0200 add/update README(s) commit 8015cf3 Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 10:40:50 2025 +0200 add/update CITATION.cff commit 60a4723 Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 10:38:00 2025 +0200 add CITATION.cff validation as pre-commit hooks commit c2eca36 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 11:24:24 2025 +0200 add IDs to table and make pipeline work again commit a98137c Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:24:31 2025 +0200 add citations file to UMCG dataset commit 819d83f Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:15:41 2025 +0200 Revert "move licenses" This reverts commit f7a6ae3. commit f7a6ae3 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:15:01 2025 +0200 move licenses commit 61e456d Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:13:57 2025 +0200 improve legal framework commit 5b36333 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 09:48:30 2025 +0200 small fix in readme templates commit 7fd4c65 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 09:30:34 2025 +0200 update readme & reorder pipeline commit 6da1d4e Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 15:57:00 2025 +0200 refactor scripts and update DVC configuration - update DVC to use latest lyscripts - update UMCG to new file path under 2025-... - remove unnecessary stages - add rendering of UMCG data README - refactor Python scripts commit fa163cb Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 15:40:13 2025 +0200 stop tracking 2025-umcg-hypopharynx-larynx/README.md commit 2c94f73 Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 13:56:24 2025 +0200 rename hypopharynx-larynx USZ data to 2025 commit 60651e6 Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 12:50:50 2025 +0200 rename UMCG data to 2025 commit c15b908 Author: Roman Ludwig <[email protected]> Date: Tue Jul 8 18:28:44 2025 +0200 add contributing guide Related: #22 commit 60cc9f0 Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 15:03:36 2025 +0200 reduce unnecessary pipeline steps & rerun commit 0b03802 Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 15:00:51 2025 +0200 recompile Python requirements & rerun pipeline commit 5049dad Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 14:57:05 2025 +0200 remove library and related files/config The library now lives in its own dedicated repo and there is no need anymore to track it here. Fixes: #20 commit d8cdb38 Author: Roman Ludwig <[email protected]> Date: Tue Jun 24 16:03:25 2025 +0200 fix: broken lyscripts docs links commit 340753e Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 14:46:37 2025 +0200 chore: update links after transfer to lycosystem commit 5876fd2 Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 13:41:41 2025 +0200 ci: rename README.template to README.md.jinja commit 85a28f0 Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 11:36:41 2025 +0200 chore: update pre-commit & ruff rules commit abc9236 Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:53:43 2025 +0100 fix missing age in last patient commit c2e87a0 Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:50:40 2025 +0100 fix missing subsite in one patient This particular patient was double checked with the people from Freiburg. commit 2f9b6fb Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:48:37 2025 +0100 add missing M0 stage for two patients commit bab314e Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:25:40 2025 +0100 add 'c' prefix to T-stage All patients where at least clinically staged, so they must all have at least a 'c' as T-stage prefix. commit 61ad709 Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 11:48:36 2025 +0100 add conflicts to pipeline commit bf0a1cd Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 11:48:14 2025 +0100 add script to plot conflicts btw modalities commit 467e856 Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 09:43:51 2025 +0100 rename `FNA` to `sonography` In a call with Dr. Rühle, he mentioned that they used `FNA` to encode a sonography diagnosis. So, we renamed that. commit 15ff90e Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:29:07 2025 +0100 remove another weird quote string commit cb605d4 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:26:32 2025 +0100 replace id with institution name commit 3841e8e Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:02:28 2025 +0100 reorder & add id nums to data.csv I applied the following commands in order: ```bash lyscripts data join --inputs ruehle.csv schaefer.csv --output joined.csv nl -b p'^,' joined.csv > numbered.csv sed 's/^[[:space:]]*\([0-9]*\)[[:space:]]*/\1/' numbered.csv > data.csv ``` commit c8de9a1 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 13:48:28 2025 +0100 concat & add id nums to ruehle & schaefer commit 9eecdfb Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:41:17 2025 +0100 make central true if position is central commit 5df4944 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:39:21 2025 +0100 remove weird string of quotes from schafer.csv commit 1db3aa8 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:37:54 2025 +0100 fix T-stage prefix and 'ambiguous' position commit 0daa185 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:34:39 2025 +0100 fix negative age in one patient commit ce4ee5b Author: Roman Ludwig <[email protected]> Date: Wed Jan 15 17:09:15 2025 +0100 add parsed CSV files from Freiburg (UKF) commit 3412f8e Author: Roman Ludwig <[email protected]> Date: Thu Apr 4 09:54:42 2024 +0200 rerun pipeline (no changes?) commit 0fb37bf Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 12:24:07 2024 +0200 add follow-up & recurrene info commit 167e6e0 Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 11:26:03 2024 +0200 fix wrong regional recurrence in one patient commit 9d95484 Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 11:00:20 2024 +0200 add distance to midline commit 63c9d1b Author: Roman Ludwig <[email protected]> Date: Mon Mar 25 16:51:21 2024 +0100 rerun pipeline commit 91fd97f Author: Roman Ludwig <[email protected]> Date: Mon Mar 25 16:45:46 2024 +0100 del C10.8 patient & change C12.9 to C12 commit 093a1a4 Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 15:22:15 2024 +0100 fix smoking & T-cat, create plots commit ff5d4ea Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 14:52:18 2024 +0100 join surgery & radiotherapy data commit b12fc36 Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 14:38:34 2024 +0100 add LNL VII to surgery patients commit 66147fc Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:49:04 2024 +0100 rerun after merge commit af74a3a Merge: a4b4210 258ce1a Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:47:55 2024 +0100 Merge branch 'tmp' into 2024-umcg-hypopharynx-larynx commit 258ce1a Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:47:17 2024 +0100 join UMCG datasets & rerun pipeline commit a4b4210 Author: rmnldwg <[email protected]> Date: Wed Feb 21 14:22:02 2024 +0100 add LNL VII to radiotherapy patients commit 52a35f5 Author: Roman Ludwig <[email protected]> Date: Tue Feb 20 09:56:55 2024 +0100 create first version of mapping of surgical data commit 56bd28a Author: rmnldwg <[email protected]> Date: Wed Feb 14 17:33:03 2024 +0100 choose earliest of dates & set unknown age to -1 commit eadff41 Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:30:22 2024 +0100 fix all True involvement commit b723519 Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:16:16 2024 +0100 fix mixxing age commit 710a34a Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:12:20 2024 +0100 add lower bound to lyscripts commit 24983ad Author: rmnldwg <[email protected]> Date: Wed Feb 14 14:50:39 2024 +0100 first successful tranformation of rad data commit c036695 Author: Roman Ludwig <[email protected]> Date: Wed Feb 14 10:46:51 2024 +0100 start writing mapping for UMCG dataset commit caecfc6 Author: Roman Ludwig <[email protected]> Date: Tue Feb 13 13:53:17 2024 +0100 update midline extension info in radiotherapy data commit b657af1 Author: rmnldwg <[email protected]> Date: Mon Feb 12 17:32:04 2024 +0100 add raw data from UMCG commit 843a895 Author: rmnldwg <[email protected]> Date: Tue Nov 21 11:06:32 2023 +0100 add id, insititution to hypo/larynx data via stage commit 23098ee Merge: c407abd 304d985 Author: rmnldwg <[email protected]> Date: Tue Nov 21 11:05:04 2023 +0100 merge: branch 'main' into '2023-usz-hypopharynx-larynx' commit c407abd Merge: 0cd41e4 29221aa Author: rmnldwg <[email protected]> Date: Tue Nov 21 09:38:52 2023 +0100 merge: branch 'main' into '2023-usz-hypopharynx-larynx' commit 0cd41e4 Author: rmnldwg <[email protected]> Date: Fri Oct 20 12:59:49 2023 +0800 fix pCT date & add consensus to patients commit 5c3d19a Author: rmnldwg <[email protected]> Date: Fri Oct 20 11:53:25 2023 +0800 create data.csv from raw parsed.csv commit 7b97ac8 Author: rmnldwg <[email protected]> Date: Thu Oct 19 13:36:20 2023 +0800 change "ambiguous" to "central" in tumor side commit 6e2575d Author: rmnldwg <[email protected]> Date: Tue Oct 17 16:20:15 2023 +0800 add parsed CSV data table
Squashed commit of the following: commit 8aca0eb66246af1c001d19256d98b84c0f31e1c8 Author: Roman Ludwig <[email protected]> Date: Wed Sep 24 11:40:24 2025 +0200 add info about squash commits commit 475eee8 Author: Roman Ludwig <[email protected]> Date: Mon Sep 22 12:27:28 2025 +0200 shift UKF dates randomly commit a4499ab Author: Roman Ludwig <[email protected]> Date: Mon Sep 22 12:22:56 2025 +0200 shift UMCG dates randomly commit c79a327 Author: Roman Ludwig <[email protected]> Date: Fri Sep 5 10:56:39 2025 +0200 remove follow-up & recurrence from UMCG data commit 90c4fce Author: Roman Ludwig <[email protected]> Date: Fri Sep 5 10:51:10 2025 +0200 remove follop-up & recurrence from UKF data commit 1909c71 Merge: 1e28727 4eb6177 Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 15:25:17 2025 +0200 Merge branch 'timeline-plot' into dev commit 4eb6177 Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 15:24:49 2025 +0200 add timeline over patients against diagnosis times commit 78b2b2f Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 14:27:16 2025 +0200 fix UMCG diagnose date in 1800 to 2018 commit d734461 Author: Roman Ludwig <[email protected]> Date: Tue Sep 2 16:41:08 2025 +0200 start working on a timeline plot commit 1e28727 Author: Roman Ludwig <[email protected]> Date: Mon Sep 1 15:22:36 2025 +0200 add UKF subsite/T-cat. area plot again commit 35c06b8 Author: Roman Ludwig <[email protected]> Date: Wed Aug 27 12:23:40 2025 +0200 add preliminary zenodo DOIs commit 3de6172 Author: Roman Ludwig <[email protected]> Date: Wed Aug 27 12:22:31 2025 +0200 change which figures to plot for new data commit bba51f3 Author: Roman Ludwig <[email protected]> Date: Tue Aug 26 10:22:18 2025 +0200 markdownlint fix jinja templates commit bcc47e4 Author: Roman Ludwig <[email protected]> Date: Tue Aug 26 10:20:22 2025 +0200 fix some typos commit 5c219f5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 13:50:14 2025 +0200 all datasets (except UMCG) cast & valid commit 8375751 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 12:27:43 2025 +0200 2023 CLB passes validation commit 0e624c4 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 12:04:40 2025 +0200 2025 USZ passes validation commit 1144d65 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:32:05 2025 +0200 cast every dataset to cleaner dtype commit 62d96c6 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:08:52 2025 +0200 fix date 12/11/!2 to 12/11/2012 in HVH data commit 32a17f9 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:03:44 2025 +0200 change 5011 to 2011 in ISB data commit b085dfa Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 14:36:13 2025 +0200 rename `stage_prefix` to `t_stage_prefix` & MX=-1 commit e68141f Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 17:41:33 2025 +0200 remove MX (-1), as it is not valid TNM stage commit ddd65ea Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 11:05:57 2025 +0200 rename `dist_mid` to `dist_to_midline` commit fc7c60d Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 09:55:37 2025 +0200 rm ukf.docx commit 292628a Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 14:30:04 2025 +0200 rm empty UKF cols & document follo-up/recurrence commit 0c3b448 Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 14:14:56 2025 +0200 add metainfor to UKF dataset commit c1be95a Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 12:55:35 2025 +0200 shift 2025-USZ dates randomly commit ad0ab7b Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 10:44:20 2025 +0200 fix location of two 2025 USZ patients commit de48e8a Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 17:02:07 2025 +0200 add hypo/larynx are plots to figures folders commit 8ca7503 Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 15:50:08 2025 +0200 add (unused) script to infer location from ICD commit c11011a Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 11:28:55 2025 +0200 fine-tune area plot commit af0016d Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 17:15:03 2025 +0200 make first version of subsite/T-stage plot commit 66daff5 Merge: ab04379 ea9d4b5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 13:55:43 2025 +0200 Merge branch '23-unique-ids' into dev commit ea9d4b5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 13:22:45 2025 +0200 add N-stage suffix to 2025-usz Also, for some patients typos were corrected. Thus, one more patient is now in the table because their ICD code was corrected. commit 6c56a63 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 17:38:56 2025 +0200 don't use -1 for MX stage, but simply `None` commit 4b519c6 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 14:09:34 2025 +0200 add unique IDs to every row Fixes: #23 commit c5993c1 Merge: ab04379 f622116 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 10:04:42 2025 +0200 Merge branch '21-change-2nd-level-headers' into dev commit f622116 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 10:00:05 2025 +0200 make every cmd use its own set of dependencies commit 08fd2bc Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 09:33:34 2025 +0200 change docs about midlvl cols to "core" commit fb55afa Author: Roman Ludwig <[email protected]> Date: Thu Jul 31 14:44:51 2025 +0200 start changing midlvl cols to "core" Some scripts aren't working yet, though. Related: #21 commit 099f4e3 Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 16:33:11 2025 +0200 add info on UKF data & reproducing pipeline commit 83654ae Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 16:14:04 2025 +0200 make scripts' deps independent using uv commit 5a96af5 Merge: c44bef4 b0456ba Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 15:08:29 2025 +0200 pin numpy dependency commit b0456ba Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 15:02:55 2025 +0200 pin numpy dependency commit c44bef4 Author: Roman Ludwig <[email protected]> Date: Fri Jul 25 11:14:06 2025 +0200 update/improve UMCG/USZ column description commit d3b511b Author: Roman Ludwig <[email protected]> Date: Wed Jul 23 08:51:45 2025 +0200 update & refactor scripts, rerun pipeline commit 894cbe1 Author: Roman Ludwig <[email protected]> Date: Tue Jul 22 17:22:36 2025 +0200 update scripts & rerun with new lyscripts commit ce2ac25 Author: Roman Ludwig <[email protected]> Date: Tue Jul 22 11:31:55 2025 +0200 rerun pipeline (figures not yet working) commit 25d04f7 Author: Roman Ludwig <[email protected]> Date: Mon Jul 21 16:43:32 2025 +0200 replace `#` and `1` with `info` in 2nd lvl headers commit ab04379 Author: Roman Ludwig <[email protected]> Date: Mon Jul 21 13:42:07 2025 +0200 generate figures for 2025-usz-... too commit fe439c2 Merge: 325b469 fbf73af Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 14:08:42 2025 +0200 merge: branch '2025-usz-hypopharynx-larynx' into 'dev' commit 325b469 Merge: 819d83f a98137c Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 13:32:54 2025 +0200 merge: branch '2025-umcg-hypopharynx-larynx' into 'dev' commit fbf73af Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 11:37:41 2025 +0200 add/update README(s) commit 8015cf3 Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 10:40:50 2025 +0200 add/update CITATION.cff commit 60a4723 Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 10:38:00 2025 +0200 add CITATION.cff validation as pre-commit hooks commit c2eca36 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 11:24:24 2025 +0200 add IDs to table and make pipeline work again commit a98137c Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:24:31 2025 +0200 add citations file to UMCG dataset commit 819d83f Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:15:41 2025 +0200 Revert "move licenses" This reverts commit f7a6ae3. commit f7a6ae3 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:15:01 2025 +0200 move licenses commit 61e456d Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:13:57 2025 +0200 improve legal framework commit 5b36333 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 09:48:30 2025 +0200 small fix in readme templates commit 7fd4c65 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 09:30:34 2025 +0200 update readme & reorder pipeline commit 6da1d4e Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 15:57:00 2025 +0200 refactor scripts and update DVC configuration - update DVC to use latest lyscripts - update UMCG to new file path under 2025-... - remove unnecessary stages - add rendering of UMCG data README - refactor Python scripts commit fa163cb Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 15:40:13 2025 +0200 stop tracking 2025-umcg-hypopharynx-larynx/README.md commit 2c94f73 Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 13:56:24 2025 +0200 rename hypopharynx-larynx USZ data to 2025 commit 60651e6 Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 12:50:50 2025 +0200 rename UMCG data to 2025 commit c15b908 Author: Roman Ludwig <[email protected]> Date: Tue Jul 8 18:28:44 2025 +0200 add contributing guide Related: #22 commit 60cc9f0 Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 15:03:36 2025 +0200 reduce unnecessary pipeline steps & rerun commit 0b03802 Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 15:00:51 2025 +0200 recompile Python requirements & rerun pipeline commit 5049dad Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 14:57:05 2025 +0200 remove library and related files/config The library now lives in its own dedicated repo and there is no need anymore to track it here. Fixes: #20 commit d8cdb38 Author: Roman Ludwig <[email protected]> Date: Tue Jun 24 16:03:25 2025 +0200 fix: broken lyscripts docs links commit 340753e Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 14:46:37 2025 +0200 chore: update links after transfer to lycosystem commit 5876fd2 Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 13:41:41 2025 +0200 ci: rename README.template to README.md.jinja commit 85a28f0 Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 11:36:41 2025 +0200 chore: update pre-commit & ruff rules commit abc9236 Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:53:43 2025 +0100 fix missing age in last patient commit c2e87a0 Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:50:40 2025 +0100 fix missing subsite in one patient This particular patient was double checked with the people from Freiburg. commit 2f9b6fb Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:48:37 2025 +0100 add missing M0 stage for two patients commit bab314e Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:25:40 2025 +0100 add 'c' prefix to T-stage All patients where at least clinically staged, so they must all have at least a 'c' as T-stage prefix. commit 61ad709 Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 11:48:36 2025 +0100 add conflicts to pipeline commit bf0a1cd Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 11:48:14 2025 +0100 add script to plot conflicts btw modalities commit 467e856 Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 09:43:51 2025 +0100 rename `FNA` to `sonography` In a call with Dr. Rühle, he mentioned that they used `FNA` to encode a sonography diagnosis. So, we renamed that. commit 15ff90e Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:29:07 2025 +0100 remove another weird quote string commit cb605d4 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:26:32 2025 +0100 replace id with institution name commit 3841e8e Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:02:28 2025 +0100 reorder & add id nums to data.csv I applied the following commands in order: ```bash lyscripts data join --inputs ruehle.csv schaefer.csv --output joined.csv nl -b p'^,' joined.csv > numbered.csv sed 's/^[[:space:]]*\([0-9]*\)[[:space:]]*/\1/' numbered.csv > data.csv ``` commit c8de9a1 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 13:48:28 2025 +0100 concat & add id nums to ruehle & schaefer commit 9eecdfb Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:41:17 2025 +0100 make central true if position is central commit 5df4944 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:39:21 2025 +0100 remove weird string of quotes from schafer.csv commit 1db3aa8 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:37:54 2025 +0100 fix T-stage prefix and 'ambiguous' position commit 0daa185 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:34:39 2025 +0100 fix negative age in one patient commit ce4ee5b Author: Roman Ludwig <[email protected]> Date: Wed Jan 15 17:09:15 2025 +0100 add parsed CSV files from Freiburg (UKF) commit 3412f8e Author: Roman Ludwig <[email protected]> Date: Thu Apr 4 09:54:42 2024 +0200 rerun pipeline (no changes?) commit 0fb37bf Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 12:24:07 2024 +0200 add follow-up & recurrene info commit 167e6e0 Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 11:26:03 2024 +0200 fix wrong regional recurrence in one patient commit 9d95484 Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 11:00:20 2024 +0200 add distance to midline commit 63c9d1b Author: Roman Ludwig <[email protected]> Date: Mon Mar 25 16:51:21 2024 +0100 rerun pipeline commit 91fd97f Author: Roman Ludwig <[email protected]> Date: Mon Mar 25 16:45:46 2024 +0100 del C10.8 patient & change C12.9 to C12 commit 093a1a4 Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 15:22:15 2024 +0100 fix smoking & T-cat, create plots commit ff5d4ea Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 14:52:18 2024 +0100 join surgery & radiotherapy data commit b12fc36 Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 14:38:34 2024 +0100 add LNL VII to surgery patients commit 66147fc Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:49:04 2024 +0100 rerun after merge commit af74a3a Merge: a4b4210 258ce1a Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:47:55 2024 +0100 Merge branch 'tmp' into 2024-umcg-hypopharynx-larynx commit 258ce1a Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:47:17 2024 +0100 join UMCG datasets & rerun pipeline commit a4b4210 Author: rmnldwg <[email protected]> Date: Wed Feb 21 14:22:02 2024 +0100 add LNL VII to radiotherapy patients commit 52a35f5 Author: Roman Ludwig <[email protected]> Date: Tue Feb 20 09:56:55 2024 +0100 create first version of mapping of surgical data commit 56bd28a Author: rmnldwg <[email protected]> Date: Wed Feb 14 17:33:03 2024 +0100 choose earliest of dates & set unknown age to -1 commit eadff41 Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:30:22 2024 +0100 fix all True involvement commit b723519 Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:16:16 2024 +0100 fix mixxing age commit 710a34a Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:12:20 2024 +0100 add lower bound to lyscripts commit 24983ad Author: rmnldwg <[email protected]> Date: Wed Feb 14 14:50:39 2024 +0100 first successful tranformation of rad data commit c036695 Author: Roman Ludwig <[email protected]> Date: Wed Feb 14 10:46:51 2024 +0100 start writing mapping for UMCG dataset commit caecfc6 Author: Roman Ludwig <[email protected]> Date: Tue Feb 13 13:53:17 2024 +0100 update midline extension info in radiotherapy data commit b657af1 Author: rmnldwg <[email protected]> Date: Mon Feb 12 17:32:04 2024 +0100 add raw data from UMCG commit 843a895 Author: rmnldwg <[email protected]> Date: Tue Nov 21 11:06:32 2023 +0100 add id, insititution to hypo/larynx data via stage commit 23098ee Merge: c407abd 304d985 Author: rmnldwg <[email protected]> Date: Tue Nov 21 11:05:04 2023 +0100 merge: branch 'main' into '2023-usz-hypopharynx-larynx' commit c407abd Merge: 0cd41e4 29221aa Author: rmnldwg <[email protected]> Date: Tue Nov 21 09:38:52 2023 +0100 merge: branch 'main' into '2023-usz-hypopharynx-larynx' commit 0cd41e4 Author: rmnldwg <[email protected]> Date: Fri Oct 20 12:59:49 2023 +0800 fix pCT date & add consensus to patients commit 5c3d19a Author: rmnldwg <[email protected]> Date: Fri Oct 20 11:53:25 2023 +0800 create data.csv from raw parsed.csv commit 7b97ac8 Author: rmnldwg <[email protected]> Date: Thu Oct 19 13:36:20 2023 +0800 change "ambiguous" to "central" in tumor side commit 6e2575d Author: rmnldwg <[email protected]> Date: Tue Oct 17 16:20:15 2023 +0800 add parsed CSV data table
Squashed commit of the following: commit 8aca0eb66246af1c001d19256d98b84c0f31e1c8 Author: Roman Ludwig <[email protected]> Date: Wed Sep 24 11:40:24 2025 +0200 add info about squash commits commit 475eee8 Author: Roman Ludwig <[email protected]> Date: Mon Sep 22 12:27:28 2025 +0200 shift UKF dates randomly commit a4499ab Author: Roman Ludwig <[email protected]> Date: Mon Sep 22 12:22:56 2025 +0200 shift UMCG dates randomly commit c79a327 Author: Roman Ludwig <[email protected]> Date: Fri Sep 5 10:56:39 2025 +0200 remove follow-up & recurrence from UMCG data commit 90c4fce Author: Roman Ludwig <[email protected]> Date: Fri Sep 5 10:51:10 2025 +0200 remove follop-up & recurrence from UKF data commit 1909c71 Merge: 1e28727 4eb6177 Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 15:25:17 2025 +0200 Merge branch 'timeline-plot' into dev commit 4eb6177 Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 15:24:49 2025 +0200 add timeline over patients against diagnosis times commit 78b2b2f Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 14:27:16 2025 +0200 fix UMCG diagnose date in 1800 to 2018 commit d734461 Author: Roman Ludwig <[email protected]> Date: Tue Sep 2 16:41:08 2025 +0200 start working on a timeline plot commit 1e28727 Author: Roman Ludwig <[email protected]> Date: Mon Sep 1 15:22:36 2025 +0200 add UKF subsite/T-cat. area plot again commit 35c06b8 Author: Roman Ludwig <[email protected]> Date: Wed Aug 27 12:23:40 2025 +0200 add preliminary zenodo DOIs commit 3de6172 Author: Roman Ludwig <[email protected]> Date: Wed Aug 27 12:22:31 2025 +0200 change which figures to plot for new data commit bba51f3 Author: Roman Ludwig <[email protected]> Date: Tue Aug 26 10:22:18 2025 +0200 markdownlint fix jinja templates commit bcc47e4 Author: Roman Ludwig <[email protected]> Date: Tue Aug 26 10:20:22 2025 +0200 fix some typos commit 5c219f5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 13:50:14 2025 +0200 all datasets (except UMCG) cast & valid commit 8375751 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 12:27:43 2025 +0200 2023 CLB passes validation commit 0e624c4 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 12:04:40 2025 +0200 2025 USZ passes validation commit 1144d65 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:32:05 2025 +0200 cast every dataset to cleaner dtype commit 62d96c6 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:08:52 2025 +0200 fix date 12/11/!2 to 12/11/2012 in HVH data commit 32a17f9 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:03:44 2025 +0200 change 5011 to 2011 in ISB data commit b085dfa Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 14:36:13 2025 +0200 rename `stage_prefix` to `t_stage_prefix` & MX=-1 commit e68141f Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 17:41:33 2025 +0200 remove MX (-1), as it is not valid TNM stage commit ddd65ea Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 11:05:57 2025 +0200 rename `dist_mid` to `dist_to_midline` commit fc7c60d Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 09:55:37 2025 +0200 rm ukf.docx commit 292628a Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 14:30:04 2025 +0200 rm empty UKF cols & document follo-up/recurrence commit 0c3b448 Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 14:14:56 2025 +0200 add metainfor to UKF dataset commit c1be95a Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 12:55:35 2025 +0200 shift 2025-USZ dates randomly commit ad0ab7b Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 10:44:20 2025 +0200 fix location of two 2025 USZ patients commit de48e8a Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 17:02:07 2025 +0200 add hypo/larynx are plots to figures folders commit 8ca7503 Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 15:50:08 2025 +0200 add (unused) script to infer location from ICD commit c11011a Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 11:28:55 2025 +0200 fine-tune area plot commit af0016d Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 17:15:03 2025 +0200 make first version of subsite/T-stage plot commit 66daff5 Merge: ab04379 ea9d4b5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 13:55:43 2025 +0200 Merge branch '23-unique-ids' into dev commit ea9d4b5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 13:22:45 2025 +0200 add N-stage suffix to 2025-usz Also, for some patients typos were corrected. Thus, one more patient is now in the table because their ICD code was corrected. commit 6c56a63 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 17:38:56 2025 +0200 don't use -1 for MX stage, but simply `None` commit 4b519c6 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 14:09:34 2025 +0200 add unique IDs to every row Fixes: #23 commit c5993c1 Merge: ab04379 f622116 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 10:04:42 2025 +0200 Merge branch '21-change-2nd-level-headers' into dev commit f622116 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 10:00:05 2025 +0200 make every cmd use its own set of dependencies commit 08fd2bc Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 09:33:34 2025 +0200 change docs about midlvl cols to "core" commit fb55afa Author: Roman Ludwig <[email protected]> Date: Thu Jul 31 14:44:51 2025 +0200 start changing midlvl cols to "core" Some scripts aren't working yet, though. Related: #21 commit 099f4e3 Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 16:33:11 2025 +0200 add info on UKF data & reproducing pipeline commit 83654ae Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 16:14:04 2025 +0200 make scripts' deps independent using uv commit 5a96af5 Merge: c44bef4 b0456ba Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 15:08:29 2025 +0200 pin numpy dependency commit b0456ba Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 15:02:55 2025 +0200 pin numpy dependency commit c44bef4 Author: Roman Ludwig <[email protected]> Date: Fri Jul 25 11:14:06 2025 +0200 update/improve UMCG/USZ column description commit d3b511b Author: Roman Ludwig <[email protected]> Date: Wed Jul 23 08:51:45 2025 +0200 update & refactor scripts, rerun pipeline commit 894cbe1 Author: Roman Ludwig <[email protected]> Date: Tue Jul 22 17:22:36 2025 +0200 update scripts & rerun with new lyscripts commit ce2ac25 Author: Roman Ludwig <[email protected]> Date: Tue Jul 22 11:31:55 2025 +0200 rerun pipeline (figures not yet working) commit 25d04f7 Author: Roman Ludwig <[email protected]> Date: Mon Jul 21 16:43:32 2025 +0200 replace `#` and `1` with `info` in 2nd lvl headers commit ab04379 Author: Roman Ludwig <[email protected]> Date: Mon Jul 21 13:42:07 2025 +0200 generate figures for 2025-usz-... too commit fe439c2 Merge: 325b469 fbf73af Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 14:08:42 2025 +0200 merge: branch '2025-usz-hypopharynx-larynx' into 'dev' commit 325b469 Merge: 819d83f a98137c Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 13:32:54 2025 +0200 merge: branch '2025-umcg-hypopharynx-larynx' into 'dev' commit fbf73af Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 11:37:41 2025 +0200 add/update README(s) commit 8015cf3 Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 10:40:50 2025 +0200 add/update CITATION.cff commit 60a4723 Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 10:38:00 2025 +0200 add CITATION.cff validation as pre-commit hooks commit c2eca36 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 11:24:24 2025 +0200 add IDs to table and make pipeline work again commit a98137c Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:24:31 2025 +0200 add citations file to UMCG dataset commit 819d83f Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:15:41 2025 +0200 Revert "move licenses" This reverts commit f7a6ae3. commit f7a6ae3 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:15:01 2025 +0200 move licenses commit 61e456d Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:13:57 2025 +0200 improve legal framework commit 5b36333 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 09:48:30 2025 +0200 small fix in readme templates commit 7fd4c65 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 09:30:34 2025 +0200 update readme & reorder pipeline commit 6da1d4e Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 15:57:00 2025 +0200 refactor scripts and update DVC configuration - update DVC to use latest lyscripts - update UMCG to new file path under 2025-... - remove unnecessary stages - add rendering of UMCG data README - refactor Python scripts commit fa163cb Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 15:40:13 2025 +0200 stop tracking 2025-umcg-hypopharynx-larynx/README.md commit 2c94f73 Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 13:56:24 2025 +0200 rename hypopharynx-larynx USZ data to 2025 commit 60651e6 Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 12:50:50 2025 +0200 rename UMCG data to 2025 commit c15b908 Author: Roman Ludwig <[email protected]> Date: Tue Jul 8 18:28:44 2025 +0200 add contributing guide Related: #22 commit 60cc9f0 Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 15:03:36 2025 +0200 reduce unnecessary pipeline steps & rerun commit 0b03802 Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 15:00:51 2025 +0200 recompile Python requirements & rerun pipeline commit 5049dad Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 14:57:05 2025 +0200 remove library and related files/config The library now lives in its own dedicated repo and there is no need anymore to track it here. Fixes: #20 commit d8cdb38 Author: Roman Ludwig <[email protected]> Date: Tue Jun 24 16:03:25 2025 +0200 fix: broken lyscripts docs links commit 340753e Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 14:46:37 2025 +0200 chore: update links after transfer to lycosystem commit 5876fd2 Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 13:41:41 2025 +0200 ci: rename README.template to README.md.jinja commit 85a28f0 Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 11:36:41 2025 +0200 chore: update pre-commit & ruff rules commit abc9236 Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:53:43 2025 +0100 fix missing age in last patient commit c2e87a0 Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:50:40 2025 +0100 fix missing subsite in one patient This particular patient was double checked with the people from Freiburg. commit 2f9b6fb Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:48:37 2025 +0100 add missing M0 stage for two patients commit bab314e Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:25:40 2025 +0100 add 'c' prefix to T-stage All patients where at least clinically staged, so they must all have at least a 'c' as T-stage prefix. commit 61ad709 Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 11:48:36 2025 +0100 add conflicts to pipeline commit bf0a1cd Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 11:48:14 2025 +0100 add script to plot conflicts btw modalities commit 467e856 Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 09:43:51 2025 +0100 rename `FNA` to `sonography` In a call with Dr. Rühle, he mentioned that they used `FNA` to encode a sonography diagnosis. So, we renamed that. commit 15ff90e Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:29:07 2025 +0100 remove another weird quote string commit cb605d4 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:26:32 2025 +0100 replace id with institution name commit 3841e8e Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:02:28 2025 +0100 reorder & add id nums to data.csv I applied the following commands in order: ```bash lyscripts data join --inputs ruehle.csv schaefer.csv --output joined.csv nl -b p'^,' joined.csv > numbered.csv sed 's/^[[:space:]]*\([0-9]*\)[[:space:]]*/\1/' numbered.csv > data.csv ``` commit c8de9a1 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 13:48:28 2025 +0100 concat & add id nums to ruehle & schaefer commit 9eecdfb Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:41:17 2025 +0100 make central true if position is central commit 5df4944 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:39:21 2025 +0100 remove weird string of quotes from schafer.csv commit 1db3aa8 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:37:54 2025 +0100 fix T-stage prefix and 'ambiguous' position commit 0daa185 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:34:39 2025 +0100 fix negative age in one patient commit ce4ee5b Author: Roman Ludwig <[email protected]> Date: Wed Jan 15 17:09:15 2025 +0100 add parsed CSV files from Freiburg (UKF) commit 3412f8e Author: Roman Ludwig <[email protected]> Date: Thu Apr 4 09:54:42 2024 +0200 rerun pipeline (no changes?) commit 0fb37bf Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 12:24:07 2024 +0200 add follow-up & recurrene info commit 167e6e0 Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 11:26:03 2024 +0200 fix wrong regional recurrence in one patient commit 9d95484 Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 11:00:20 2024 +0200 add distance to midline commit 63c9d1b Author: Roman Ludwig <[email protected]> Date: Mon Mar 25 16:51:21 2024 +0100 rerun pipeline commit 91fd97f Author: Roman Ludwig <[email protected]> Date: Mon Mar 25 16:45:46 2024 +0100 del C10.8 patient & change C12.9 to C12 commit 093a1a4 Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 15:22:15 2024 +0100 fix smoking & T-cat, create plots commit ff5d4ea Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 14:52:18 2024 +0100 join surgery & radiotherapy data commit b12fc36 Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 14:38:34 2024 +0100 add LNL VII to surgery patients commit 66147fc Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:49:04 2024 +0100 rerun after merge commit af74a3a Merge: a4b4210 258ce1a Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:47:55 2024 +0100 Merge branch 'tmp' into 2024-umcg-hypopharynx-larynx commit 258ce1a Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:47:17 2024 +0100 join UMCG datasets & rerun pipeline commit a4b4210 Author: rmnldwg <[email protected]> Date: Wed Feb 21 14:22:02 2024 +0100 add LNL VII to radiotherapy patients commit 52a35f5 Author: Roman Ludwig <[email protected]> Date: Tue Feb 20 09:56:55 2024 +0100 create first version of mapping of surgical data commit 56bd28a Author: rmnldwg <[email protected]> Date: Wed Feb 14 17:33:03 2024 +0100 choose earliest of dates & set unknown age to -1 commit eadff41 Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:30:22 2024 +0100 fix all True involvement commit b723519 Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:16:16 2024 +0100 fix mixxing age commit 710a34a Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:12:20 2024 +0100 add lower bound to lyscripts commit 24983ad Author: rmnldwg <[email protected]> Date: Wed Feb 14 14:50:39 2024 +0100 first successful tranformation of rad data commit c036695 Author: Roman Ludwig <[email protected]> Date: Wed Feb 14 10:46:51 2024 +0100 start writing mapping for UMCG dataset commit caecfc6 Author: Roman Ludwig <[email protected]> Date: Tue Feb 13 13:53:17 2024 +0100 update midline extension info in radiotherapy data commit b657af1 Author: rmnldwg <[email protected]> Date: Mon Feb 12 17:32:04 2024 +0100 add raw data from UMCG commit 843a895 Author: rmnldwg <[email protected]> Date: Tue Nov 21 11:06:32 2023 +0100 add id, insititution to hypo/larynx data via stage commit 23098ee Merge: c407abd 304d985 Author: rmnldwg <[email protected]> Date: Tue Nov 21 11:05:04 2023 +0100 merge: branch 'main' into '2023-usz-hypopharynx-larynx' commit c407abd Merge: 0cd41e4 29221aa Author: rmnldwg <[email protected]> Date: Tue Nov 21 09:38:52 2023 +0100 merge: branch 'main' into '2023-usz-hypopharynx-larynx' commit 0cd41e4 Author: rmnldwg <[email protected]> Date: Fri Oct 20 12:59:49 2023 +0800 fix pCT date & add consensus to patients commit 5c3d19a Author: rmnldwg <[email protected]> Date: Fri Oct 20 11:53:25 2023 +0800 create data.csv from raw parsed.csv commit 7b97ac8 Author: rmnldwg <[email protected]> Date: Thu Oct 19 13:36:20 2023 +0800 change "ambiguous" to "central" in tumor side commit 6e2575d Author: rmnldwg <[email protected]> Date: Tue Oct 17 16:20:15 2023 +0800 add parsed CSV data table
Squashed commit of the following: commit 8aca0eb66246af1c001d19256d98b84c0f31e1c8 Author: Roman Ludwig <[email protected]> Date: Wed Sep 24 11:40:24 2025 +0200 add info about squash commits commit 475eee8 Author: Roman Ludwig <[email protected]> Date: Mon Sep 22 12:27:28 2025 +0200 shift UKF dates randomly commit a4499ab Author: Roman Ludwig <[email protected]> Date: Mon Sep 22 12:22:56 2025 +0200 shift UMCG dates randomly commit c79a327 Author: Roman Ludwig <[email protected]> Date: Fri Sep 5 10:56:39 2025 +0200 remove follow-up & recurrence from UMCG data commit 90c4fce Author: Roman Ludwig <[email protected]> Date: Fri Sep 5 10:51:10 2025 +0200 remove follop-up & recurrence from UKF data commit 1909c71 Merge: 1e28727 4eb6177 Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 15:25:17 2025 +0200 Merge branch 'timeline-plot' into dev commit 4eb6177 Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 15:24:49 2025 +0200 add timeline over patients against diagnosis times commit 78b2b2f Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 14:27:16 2025 +0200 fix UMCG diagnose date in 1800 to 2018 commit d734461 Author: Roman Ludwig <[email protected]> Date: Tue Sep 2 16:41:08 2025 +0200 start working on a timeline plot commit 1e28727 Author: Roman Ludwig <[email protected]> Date: Mon Sep 1 15:22:36 2025 +0200 add UKF subsite/T-cat. area plot again commit 35c06b8 Author: Roman Ludwig <[email protected]> Date: Wed Aug 27 12:23:40 2025 +0200 add preliminary zenodo DOIs commit 3de6172 Author: Roman Ludwig <[email protected]> Date: Wed Aug 27 12:22:31 2025 +0200 change which figures to plot for new data commit bba51f3 Author: Roman Ludwig <[email protected]> Date: Tue Aug 26 10:22:18 2025 +0200 markdownlint fix jinja templates commit bcc47e4 Author: Roman Ludwig <[email protected]> Date: Tue Aug 26 10:20:22 2025 +0200 fix some typos commit 5c219f5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 13:50:14 2025 +0200 all datasets (except UMCG) cast & valid commit 8375751 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 12:27:43 2025 +0200 2023 CLB passes validation commit 0e624c4 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 12:04:40 2025 +0200 2025 USZ passes validation commit 1144d65 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:32:05 2025 +0200 cast every dataset to cleaner dtype commit 62d96c6 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:08:52 2025 +0200 fix date 12/11/!2 to 12/11/2012 in HVH data commit 32a17f9 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:03:44 2025 +0200 change 5011 to 2011 in ISB data commit b085dfa Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 14:36:13 2025 +0200 rename `stage_prefix` to `t_stage_prefix` & MX=-1 commit e68141f Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 17:41:33 2025 +0200 remove MX (-1), as it is not valid TNM stage commit ddd65ea Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 11:05:57 2025 +0200 rename `dist_mid` to `dist_to_midline` commit fc7c60d Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 09:55:37 2025 +0200 rm ukf.docx commit 292628a Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 14:30:04 2025 +0200 rm empty UKF cols & document follo-up/recurrence commit 0c3b448 Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 14:14:56 2025 +0200 add metainfor to UKF dataset commit c1be95a Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 12:55:35 2025 +0200 shift 2025-USZ dates randomly commit ad0ab7b Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 10:44:20 2025 +0200 fix location of two 2025 USZ patients commit de48e8a Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 17:02:07 2025 +0200 add hypo/larynx are plots to figures folders commit 8ca7503 Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 15:50:08 2025 +0200 add (unused) script to infer location from ICD commit c11011a Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 11:28:55 2025 +0200 fine-tune area plot commit af0016d Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 17:15:03 2025 +0200 make first version of subsite/T-stage plot commit 66daff5 Merge: ab04379 ea9d4b5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 13:55:43 2025 +0200 Merge branch '23-unique-ids' into dev commit ea9d4b5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 13:22:45 2025 +0200 add N-stage suffix to 2025-usz Also, for some patients typos were corrected. Thus, one more patient is now in the table because their ICD code was corrected. commit 6c56a63 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 17:38:56 2025 +0200 don't use -1 for MX stage, but simply `None` commit 4b519c6 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 14:09:34 2025 +0200 add unique IDs to every row Fixes: #23 commit c5993c1 Merge: ab04379 f622116 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 10:04:42 2025 +0200 Merge branch '21-change-2nd-level-headers' into dev commit f622116 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 10:00:05 2025 +0200 make every cmd use its own set of dependencies commit 08fd2bc Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 09:33:34 2025 +0200 change docs about midlvl cols to "core" commit fb55afa Author: Roman Ludwig <[email protected]> Date: Thu Jul 31 14:44:51 2025 +0200 start changing midlvl cols to "core" Some scripts aren't working yet, though. Related: #21 commit 099f4e3 Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 16:33:11 2025 +0200 add info on UKF data & reproducing pipeline commit 83654ae Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 16:14:04 2025 +0200 make scripts' deps independent using uv commit 5a96af5 Merge: c44bef4 b0456ba Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 15:08:29 2025 +0200 pin numpy dependency commit b0456ba Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 15:02:55 2025 +0200 pin numpy dependency commit c44bef4 Author: Roman Ludwig <[email protected]> Date: Fri Jul 25 11:14:06 2025 +0200 update/improve UMCG/USZ column description commit d3b511b Author: Roman Ludwig <[email protected]> Date: Wed Jul 23 08:51:45 2025 +0200 update & refactor scripts, rerun pipeline commit 894cbe1 Author: Roman Ludwig <[email protected]> Date: Tue Jul 22 17:22:36 2025 +0200 update scripts & rerun with new lyscripts commit ce2ac25 Author: Roman Ludwig <[email protected]> Date: Tue Jul 22 11:31:55 2025 +0200 rerun pipeline (figures not yet working) commit 25d04f7 Author: Roman Ludwig <[email protected]> Date: Mon Jul 21 16:43:32 2025 +0200 replace `#` and `1` with `info` in 2nd lvl headers commit ab04379 Author: Roman Ludwig <[email protected]> Date: Mon Jul 21 13:42:07 2025 +0200 generate figures for 2025-usz-... too commit fe439c2 Merge: 325b469 fbf73af Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 14:08:42 2025 +0200 merge: branch '2025-usz-hypopharynx-larynx' into 'dev' commit 325b469 Merge: 819d83f a98137c Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 13:32:54 2025 +0200 merge: branch '2025-umcg-hypopharynx-larynx' into 'dev' commit fbf73af Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 11:37:41 2025 +0200 add/update README(s) commit 8015cf3 Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 10:40:50 2025 +0200 add/update CITATION.cff commit 60a4723 Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 10:38:00 2025 +0200 add CITATION.cff validation as pre-commit hooks commit c2eca36 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 11:24:24 2025 +0200 add IDs to table and make pipeline work again commit a98137c Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:24:31 2025 +0200 add citations file to UMCG dataset commit 819d83f Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:15:41 2025 +0200 Revert "move licenses" This reverts commit f7a6ae3. commit f7a6ae3 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:15:01 2025 +0200 move licenses commit 61e456d Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:13:57 2025 +0200 improve legal framework commit 5b36333 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 09:48:30 2025 +0200 small fix in readme templates commit 7fd4c65 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 09:30:34 2025 +0200 update readme & reorder pipeline commit 6da1d4e Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 15:57:00 2025 +0200 refactor scripts and update DVC configuration - update DVC to use latest lyscripts - update UMCG to new file path under 2025-... - remove unnecessary stages - add rendering of UMCG data README - refactor Python scripts commit fa163cb Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 15:40:13 2025 +0200 stop tracking 2025-umcg-hypopharynx-larynx/README.md commit 2c94f73 Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 13:56:24 2025 +0200 rename hypopharynx-larynx USZ data to 2025 commit 60651e6 Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 12:50:50 2025 +0200 rename UMCG data to 2025 commit c15b908 Author: Roman Ludwig <[email protected]> Date: Tue Jul 8 18:28:44 2025 +0200 add contributing guide Related: #22 commit 60cc9f0 Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 15:03:36 2025 +0200 reduce unnecessary pipeline steps & rerun commit 0b03802 Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 15:00:51 2025 +0200 recompile Python requirements & rerun pipeline commit 5049dad Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 14:57:05 2025 +0200 remove library and related files/config The library now lives in its own dedicated repo and there is no need anymore to track it here. Fixes: #20 commit d8cdb38 Author: Roman Ludwig <[email protected]> Date: Tue Jun 24 16:03:25 2025 +0200 fix: broken lyscripts docs links commit 340753e Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 14:46:37 2025 +0200 chore: update links after transfer to lycosystem commit 5876fd2 Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 13:41:41 2025 +0200 ci: rename README.template to README.md.jinja commit 85a28f0 Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 11:36:41 2025 +0200 chore: update pre-commit & ruff rules commit abc9236 Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:53:43 2025 +0100 fix missing age in last patient commit c2e87a0 Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:50:40 2025 +0100 fix missing subsite in one patient This particular patient was double checked with the people from Freiburg. commit 2f9b6fb Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:48:37 2025 +0100 add missing M0 stage for two patients commit bab314e Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:25:40 2025 +0100 add 'c' prefix to T-stage All patients where at least clinically staged, so they must all have at least a 'c' as T-stage prefix. commit 61ad709 Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 11:48:36 2025 +0100 add conflicts to pipeline commit bf0a1cd Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 11:48:14 2025 +0100 add script to plot conflicts btw modalities commit 467e856 Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 09:43:51 2025 +0100 rename `FNA` to `sonography` In a call with Dr. Rühle, he mentioned that they used `FNA` to encode a sonography diagnosis. So, we renamed that. commit 15ff90e Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:29:07 2025 +0100 remove another weird quote string commit cb605d4 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:26:32 2025 +0100 replace id with institution name commit 3841e8e Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:02:28 2025 +0100 reorder & add id nums to data.csv I applied the following commands in order: ```bash lyscripts data join --inputs ruehle.csv schaefer.csv --output joined.csv nl -b p'^,' joined.csv > numbered.csv sed 's/^[[:space:]]*\([0-9]*\)[[:space:]]*/\1/' numbered.csv > data.csv ``` commit c8de9a1 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 13:48:28 2025 +0100 concat & add id nums to ruehle & schaefer commit 9eecdfb Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:41:17 2025 +0100 make central true if position is central commit 5df4944 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:39:21 2025 +0100 remove weird string of quotes from schafer.csv commit 1db3aa8 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:37:54 2025 +0100 fix T-stage prefix and 'ambiguous' position commit 0daa185 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:34:39 2025 +0100 fix negative age in one patient commit ce4ee5b Author: Roman Ludwig <[email protected]> Date: Wed Jan 15 17:09:15 2025 +0100 add parsed CSV files from Freiburg (UKF) commit 3412f8e Author: Roman Ludwig <[email protected]> Date: Thu Apr 4 09:54:42 2024 +0200 rerun pipeline (no changes?) commit 0fb37bf Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 12:24:07 2024 +0200 add follow-up & recurrene info commit 167e6e0 Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 11:26:03 2024 +0200 fix wrong regional recurrence in one patient commit 9d95484 Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 11:00:20 2024 +0200 add distance to midline commit 63c9d1b Author: Roman Ludwig <[email protected]> Date: Mon Mar 25 16:51:21 2024 +0100 rerun pipeline commit 91fd97f Author: Roman Ludwig <[email protected]> Date: Mon Mar 25 16:45:46 2024 +0100 del C10.8 patient & change C12.9 to C12 commit 093a1a4 Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 15:22:15 2024 +0100 fix smoking & T-cat, create plots commit ff5d4ea Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 14:52:18 2024 +0100 join surgery & radiotherapy data commit b12fc36 Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 14:38:34 2024 +0100 add LNL VII to surgery patients commit 66147fc Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:49:04 2024 +0100 rerun after merge commit af74a3a Merge: a4b4210 258ce1a Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:47:55 2024 +0100 Merge branch 'tmp' into 2024-umcg-hypopharynx-larynx commit 258ce1a Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:47:17 2024 +0100 join UMCG datasets & rerun pipeline commit a4b4210 Author: rmnldwg <[email protected]> Date: Wed Feb 21 14:22:02 2024 +0100 add LNL VII to radiotherapy patients commit 52a35f5 Author: Roman Ludwig <[email protected]> Date: Tue Feb 20 09:56:55 2024 +0100 create first version of mapping of surgical data commit 56bd28a Author: rmnldwg <[email protected]> Date: Wed Feb 14 17:33:03 2024 +0100 choose earliest of dates & set unknown age to -1 commit eadff41 Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:30:22 2024 +0100 fix all True involvement commit b723519 Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:16:16 2024 +0100 fix mixxing age commit 710a34a Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:12:20 2024 +0100 add lower bound to lyscripts commit 24983ad Author: rmnldwg <[email protected]> Date: Wed Feb 14 14:50:39 2024 +0100 first successful tranformation of rad data commit c036695 Author: Roman Ludwig <[email protected]> Date: Wed Feb 14 10:46:51 2024 +0100 start writing mapping for UMCG dataset commit caecfc6 Author: Roman Ludwig <[email protected]> Date: Tue Feb 13 13:53:17 2024 +0100 update midline extension info in radiotherapy data commit b657af1 Author: rmnldwg <[email protected]> Date: Mon Feb 12 17:32:04 2024 +0100 add raw data from UMCG commit 843a895 Author: rmnldwg <[email protected]> Date: Tue Nov 21 11:06:32 2023 +0100 add id, insititution to hypo/larynx data via stage commit 23098ee Merge: c407abd 304d985 Author: rmnldwg <[email protected]> Date: Tue Nov 21 11:05:04 2023 +0100 merge: branch 'main' into '2023-usz-hypopharynx-larynx' commit c407abd Merge: 0cd41e4 29221aa Author: rmnldwg <[email protected]> Date: Tue Nov 21 09:38:52 2023 +0100 merge: branch 'main' into '2023-usz-hypopharynx-larynx' commit 0cd41e4 Author: rmnldwg <[email protected]> Date: Fri Oct 20 12:59:49 2023 +0800 fix pCT date & add consensus to patients commit 5c3d19a Author: rmnldwg <[email protected]> Date: Fri Oct 20 11:53:25 2023 +0800 create data.csv from raw parsed.csv commit 7b97ac8 Author: rmnldwg <[email protected]> Date: Thu Oct 19 13:36:20 2023 +0800 change "ambiguous" to "central" in tumor side commit 6e2575d Author: rmnldwg <[email protected]> Date: Tue Oct 17 16:20:15 2023 +0800 add parsed CSV data table
Squashed commit of the following: commit 8aca0eb66246af1c001d19256d98b84c0f31e1c8 Author: Roman Ludwig <[email protected]> Date: Wed Sep 24 11:40:24 2025 +0200 add info about squash commits commit 475eee8 Author: Roman Ludwig <[email protected]> Date: Mon Sep 22 12:27:28 2025 +0200 shift UKF dates randomly commit a4499ab Author: Roman Ludwig <[email protected]> Date: Mon Sep 22 12:22:56 2025 +0200 shift UMCG dates randomly commit c79a327 Author: Roman Ludwig <[email protected]> Date: Fri Sep 5 10:56:39 2025 +0200 remove follow-up & recurrence from UMCG data commit 90c4fce Author: Roman Ludwig <[email protected]> Date: Fri Sep 5 10:51:10 2025 +0200 remove follop-up & recurrence from UKF data commit 1909c71 Merge: 1e28727 4eb6177 Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 15:25:17 2025 +0200 Merge branch 'timeline-plot' into dev commit 4eb6177 Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 15:24:49 2025 +0200 add timeline over patients against diagnosis times commit 78b2b2f Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 14:27:16 2025 +0200 fix UMCG diagnose date in 1800 to 2018 commit d734461 Author: Roman Ludwig <[email protected]> Date: Tue Sep 2 16:41:08 2025 +0200 start working on a timeline plot commit 1e28727 Author: Roman Ludwig <[email protected]> Date: Mon Sep 1 15:22:36 2025 +0200 add UKF subsite/T-cat. area plot again commit 35c06b8 Author: Roman Ludwig <[email protected]> Date: Wed Aug 27 12:23:40 2025 +0200 add preliminary zenodo DOIs commit 3de6172 Author: Roman Ludwig <[email protected]> Date: Wed Aug 27 12:22:31 2025 +0200 change which figures to plot for new data commit bba51f3 Author: Roman Ludwig <[email protected]> Date: Tue Aug 26 10:22:18 2025 +0200 markdownlint fix jinja templates commit bcc47e4 Author: Roman Ludwig <[email protected]> Date: Tue Aug 26 10:20:22 2025 +0200 fix some typos commit 5c219f5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 13:50:14 2025 +0200 all datasets (except UMCG) cast & valid commit 8375751 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 12:27:43 2025 +0200 2023 CLB passes validation commit 0e624c4 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 12:04:40 2025 +0200 2025 USZ passes validation commit 1144d65 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:32:05 2025 +0200 cast every dataset to cleaner dtype commit 62d96c6 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:08:52 2025 +0200 fix date 12/11/!2 to 12/11/2012 in HVH data commit 32a17f9 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:03:44 2025 +0200 change 5011 to 2011 in ISB data commit b085dfa Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 14:36:13 2025 +0200 rename `stage_prefix` to `t_stage_prefix` & MX=-1 commit e68141f Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 17:41:33 2025 +0200 remove MX (-1), as it is not valid TNM stage commit ddd65ea Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 11:05:57 2025 +0200 rename `dist_mid` to `dist_to_midline` commit fc7c60d Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 09:55:37 2025 +0200 rm ukf.docx commit 292628a Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 14:30:04 2025 +0200 rm empty UKF cols & document follo-up/recurrence commit 0c3b448 Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 14:14:56 2025 +0200 add metainfor to UKF dataset commit c1be95a Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 12:55:35 2025 +0200 shift 2025-USZ dates randomly commit ad0ab7b Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 10:44:20 2025 +0200 fix location of two 2025 USZ patients commit de48e8a Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 17:02:07 2025 +0200 add hypo/larynx are plots to figures folders commit 8ca7503 Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 15:50:08 2025 +0200 add (unused) script to infer location from ICD commit c11011a Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 11:28:55 2025 +0200 fine-tune area plot commit af0016d Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 17:15:03 2025 +0200 make first version of subsite/T-stage plot commit 66daff5 Merge: ab04379 ea9d4b5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 13:55:43 2025 +0200 Merge branch '23-unique-ids' into dev commit ea9d4b5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 13:22:45 2025 +0200 add N-stage suffix to 2025-usz Also, for some patients typos were corrected. Thus, one more patient is now in the table because their ICD code was corrected. commit 6c56a63 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 17:38:56 2025 +0200 don't use -1 for MX stage, but simply `None` commit 4b519c6 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 14:09:34 2025 +0200 add unique IDs to every row Fixes: #23 commit c5993c1 Merge: ab04379 f622116 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 10:04:42 2025 +0200 Merge branch '21-change-2nd-level-headers' into dev commit f622116 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 10:00:05 2025 +0200 make every cmd use its own set of dependencies commit 08fd2bc Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 09:33:34 2025 +0200 change docs about midlvl cols to "core" commit fb55afa Author: Roman Ludwig <[email protected]> Date: Thu Jul 31 14:44:51 2025 +0200 start changing midlvl cols to "core" Some scripts aren't working yet, though. Related: #21 commit 099f4e3 Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 16:33:11 2025 +0200 add info on UKF data & reproducing pipeline commit 83654ae Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 16:14:04 2025 +0200 make scripts' deps independent using uv commit 5a96af5 Merge: c44bef4 b0456ba Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 15:08:29 2025 +0200 pin numpy dependency commit b0456ba Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 15:02:55 2025 +0200 pin numpy dependency commit c44bef4 Author: Roman Ludwig <[email protected]> Date: Fri Jul 25 11:14:06 2025 +0200 update/improve UMCG/USZ column description commit d3b511b Author: Roman Ludwig <[email protected]> Date: Wed Jul 23 08:51:45 2025 +0200 update & refactor scripts, rerun pipeline commit 894cbe1 Author: Roman Ludwig <[email protected]> Date: Tue Jul 22 17:22:36 2025 +0200 update scripts & rerun with new lyscripts commit ce2ac25 Author: Roman Ludwig <[email protected]> Date: Tue Jul 22 11:31:55 2025 +0200 rerun pipeline (figures not yet working) commit 25d04f7 Author: Roman Ludwig <[email protected]> Date: Mon Jul 21 16:43:32 2025 +0200 replace `#` and `1` with `info` in 2nd lvl headers commit ab04379 Author: Roman Ludwig <[email protected]> Date: Mon Jul 21 13:42:07 2025 +0200 generate figures for 2025-usz-... too commit fe439c2 Merge: 325b469 fbf73af Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 14:08:42 2025 +0200 merge: branch '2025-usz-hypopharynx-larynx' into 'dev' commit 325b469 Merge: 819d83f a98137c Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 13:32:54 2025 +0200 merge: branch '2025-umcg-hypopharynx-larynx' into 'dev' commit fbf73af Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 11:37:41 2025 +0200 add/update README(s) commit 8015cf3 Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 10:40:50 2025 +0200 add/update CITATION.cff commit 60a4723 Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 10:38:00 2025 +0200 add CITATION.cff validation as pre-commit hooks commit c2eca36 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 11:24:24 2025 +0200 add IDs to table and make pipeline work again commit a98137c Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:24:31 2025 +0200 add citations file to UMCG dataset commit 819d83f Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:15:41 2025 +0200 Revert "move licenses" This reverts commit f7a6ae3. commit f7a6ae3 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:15:01 2025 +0200 move licenses commit 61e456d Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:13:57 2025 +0200 improve legal framework commit 5b36333 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 09:48:30 2025 +0200 small fix in readme templates commit 7fd4c65 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 09:30:34 2025 +0200 update readme & reorder pipeline commit 6da1d4e Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 15:57:00 2025 +0200 refactor scripts and update DVC configuration - update DVC to use latest lyscripts - update UMCG to new file path under 2025-... - remove unnecessary stages - add rendering of UMCG data README - refactor Python scripts commit fa163cb Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 15:40:13 2025 +0200 stop tracking 2025-umcg-hypopharynx-larynx/README.md commit 2c94f73 Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 13:56:24 2025 +0200 rename hypopharynx-larynx USZ data to 2025 commit 60651e6 Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 12:50:50 2025 +0200 rename UMCG data to 2025 commit c15b908 Author: Roman Ludwig <[email protected]> Date: Tue Jul 8 18:28:44 2025 +0200 add contributing guide Related: #22 commit 60cc9f0 Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 15:03:36 2025 +0200 reduce unnecessary pipeline steps & rerun commit 0b03802 Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 15:00:51 2025 +0200 recompile Python requirements & rerun pipeline commit 5049dad Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 14:57:05 2025 +0200 remove library and related files/config The library now lives in its own dedicated repo and there is no need anymore to track it here. Fixes: #20 commit d8cdb38 Author: Roman Ludwig <[email protected]> Date: Tue Jun 24 16:03:25 2025 +0200 fix: broken lyscripts docs links commit 340753e Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 14:46:37 2025 +0200 chore: update links after transfer to lycosystem commit 5876fd2 Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 13:41:41 2025 +0200 ci: rename README.template to README.md.jinja commit 85a28f0 Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 11:36:41 2025 +0200 chore: update pre-commit & ruff rules commit abc9236 Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:53:43 2025 +0100 fix missing age in last patient commit c2e87a0 Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:50:40 2025 +0100 fix missing subsite in one patient This particular patient was double checked with the people from Freiburg. commit 2f9b6fb Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:48:37 2025 +0100 add missing M0 stage for two patients commit bab314e Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:25:40 2025 +0100 add 'c' prefix to T-stage All patients where at least clinically staged, so they must all have at least a 'c' as T-stage prefix. commit 61ad709 Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 11:48:36 2025 +0100 add conflicts to pipeline commit bf0a1cd Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 11:48:14 2025 +0100 add script to plot conflicts btw modalities commit 467e856 Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 09:43:51 2025 +0100 rename `FNA` to `sonography` In a call with Dr. Rühle, he mentioned that they used `FNA` to encode a sonography diagnosis. So, we renamed that. commit 15ff90e Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:29:07 2025 +0100 remove another weird quote string commit cb605d4 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:26:32 2025 +0100 replace id with institution name commit 3841e8e Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:02:28 2025 +0100 reorder & add id nums to data.csv I applied the following commands in order: ```bash lyscripts data join --inputs ruehle.csv schaefer.csv --output joined.csv nl -b p'^,' joined.csv > numbered.csv sed 's/^[[:space:]]*\([0-9]*\)[[:space:]]*/\1/' numbered.csv > data.csv ``` commit c8de9a1 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 13:48:28 2025 +0100 concat & add id nums to ruehle & schaefer commit 9eecdfb Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:41:17 2025 +0100 make central true if position is central commit 5df4944 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:39:21 2025 +0100 remove weird string of quotes from schafer.csv commit 1db3aa8 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:37:54 2025 +0100 fix T-stage prefix and 'ambiguous' position commit 0daa185 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:34:39 2025 +0100 fix negative age in one patient commit ce4ee5b Author: Roman Ludwig <[email protected]> Date: Wed Jan 15 17:09:15 2025 +0100 add parsed CSV files from Freiburg (UKF) commit 3412f8e Author: Roman Ludwig <[email protected]> Date: Thu Apr 4 09:54:42 2024 +0200 rerun pipeline (no changes?) commit 0fb37bf Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 12:24:07 2024 +0200 add follow-up & recurrene info commit 167e6e0 Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 11:26:03 2024 +0200 fix wrong regional recurrence in one patient commit 9d95484 Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 11:00:20 2024 +0200 add distance to midline commit 63c9d1b Author: Roman Ludwig <[email protected]> Date: Mon Mar 25 16:51:21 2024 +0100 rerun pipeline commit 91fd97f Author: Roman Ludwig <[email protected]> Date: Mon Mar 25 16:45:46 2024 +0100 del C10.8 patient & change C12.9 to C12 commit 093a1a4 Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 15:22:15 2024 +0100 fix smoking & T-cat, create plots commit ff5d4ea Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 14:52:18 2024 +0100 join surgery & radiotherapy data commit b12fc36 Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 14:38:34 2024 +0100 add LNL VII to surgery patients commit 66147fc Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:49:04 2024 +0100 rerun after merge commit af74a3a Merge: a4b4210 258ce1a Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:47:55 2024 +0100 Merge branch 'tmp' into 2024-umcg-hypopharynx-larynx commit 258ce1a Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:47:17 2024 +0100 join UMCG datasets & rerun pipeline commit a4b4210 Author: rmnldwg <[email protected]> Date: Wed Feb 21 14:22:02 2024 +0100 add LNL VII to radiotherapy patients commit 52a35f5 Author: Roman Ludwig <[email protected]> Date: Tue Feb 20 09:56:55 2024 +0100 create first version of mapping of surgical data commit 56bd28a Author: rmnldwg <[email protected]> Date: Wed Feb 14 17:33:03 2024 +0100 choose earliest of dates & set unknown age to -1 commit eadff41 Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:30:22 2024 +0100 fix all True involvement commit b723519 Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:16:16 2024 +0100 fix mixxing age commit 710a34a Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:12:20 2024 +0100 add lower bound to lyscripts commit 24983ad Author: rmnldwg <[email protected]> Date: Wed Feb 14 14:50:39 2024 +0100 first successful tranformation of rad data commit c036695 Author: Roman Ludwig <[email protected]> Date: Wed Feb 14 10:46:51 2024 +0100 start writing mapping for UMCG dataset commit caecfc6 Author: Roman Ludwig <[email protected]> Date: Tue Feb 13 13:53:17 2024 +0100 update midline extension info in radiotherapy data commit b657af1 Author: rmnldwg <[email protected]> Date: Mon Feb 12 17:32:04 2024 +0100 add raw data from UMCG commit 843a895 Author: rmnldwg <[email protected]> Date: Tue Nov 21 11:06:32 2023 +0100 add id, insititution to hypo/larynx data via stage commit 23098ee Merge: c407abd 304d985 Author: rmnldwg <[email protected]> Date: Tue Nov 21 11:05:04 2023 +0100 merge: branch 'main' into '2023-usz-hypopharynx-larynx' commit c407abd Merge: 0cd41e4 29221aa Author: rmnldwg <[email protected]> Date: Tue Nov 21 09:38:52 2023 +0100 merge: branch 'main' into '2023-usz-hypopharynx-larynx' commit 0cd41e4 Author: rmnldwg <[email protected]> Date: Fri Oct 20 12:59:49 2023 +0800 fix pCT date & add consensus to patients commit 5c3d19a Author: rmnldwg <[email protected]> Date: Fri Oct 20 11:53:25 2023 +0800 create data.csv from raw parsed.csv commit 7b97ac8 Author: rmnldwg <[email protected]> Date: Thu Oct 19 13:36:20 2023 +0800 change "ambiguous" to "central" in tumor side commit 6e2575d Author: rmnldwg <[email protected]> Date: Tue Oct 17 16:20:15 2023 +0800 add parsed CSV data table
Squashed commit of the following: commit 8aca0eb66246af1c001d19256d98b84c0f31e1c8 Author: Roman Ludwig <[email protected]> Date: Wed Sep 24 11:40:24 2025 +0200 add info about squash commits commit 475eee8 Author: Roman Ludwig <[email protected]> Date: Mon Sep 22 12:27:28 2025 +0200 shift UKF dates randomly commit a4499ab Author: Roman Ludwig <[email protected]> Date: Mon Sep 22 12:22:56 2025 +0200 shift UMCG dates randomly commit c79a327 Author: Roman Ludwig <[email protected]> Date: Fri Sep 5 10:56:39 2025 +0200 remove follow-up & recurrence from UMCG data commit 90c4fce Author: Roman Ludwig <[email protected]> Date: Fri Sep 5 10:51:10 2025 +0200 remove follop-up & recurrence from UKF data commit 1909c71 Merge: 1e28727 4eb6177 Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 15:25:17 2025 +0200 Merge branch 'timeline-plot' into dev commit 4eb6177 Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 15:24:49 2025 +0200 add timeline over patients against diagnosis times commit 78b2b2f Author: Roman Ludwig <[email protected]> Date: Wed Sep 3 14:27:16 2025 +0200 fix UMCG diagnose date in 1800 to 2018 commit d734461 Author: Roman Ludwig <[email protected]> Date: Tue Sep 2 16:41:08 2025 +0200 start working on a timeline plot commit 1e28727 Author: Roman Ludwig <[email protected]> Date: Mon Sep 1 15:22:36 2025 +0200 add UKF subsite/T-cat. area plot again commit 35c06b8 Author: Roman Ludwig <[email protected]> Date: Wed Aug 27 12:23:40 2025 +0200 add preliminary zenodo DOIs commit 3de6172 Author: Roman Ludwig <[email protected]> Date: Wed Aug 27 12:22:31 2025 +0200 change which figures to plot for new data commit bba51f3 Author: Roman Ludwig <[email protected]> Date: Tue Aug 26 10:22:18 2025 +0200 markdownlint fix jinja templates commit bcc47e4 Author: Roman Ludwig <[email protected]> Date: Tue Aug 26 10:20:22 2025 +0200 fix some typos commit 5c219f5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 13:50:14 2025 +0200 all datasets (except UMCG) cast & valid commit 8375751 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 12:27:43 2025 +0200 2023 CLB passes validation commit 0e624c4 Author: Roman Ludwig <[email protected]> Date: Mon Aug 25 12:04:40 2025 +0200 2025 USZ passes validation commit 1144d65 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:32:05 2025 +0200 cast every dataset to cleaner dtype commit 62d96c6 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:08:52 2025 +0200 fix date 12/11/!2 to 12/11/2012 in HVH data commit 32a17f9 Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 15:03:44 2025 +0200 change 5011 to 2011 in ISB data commit b085dfa Author: Roman Ludwig <[email protected]> Date: Fri Aug 22 14:36:13 2025 +0200 rename `stage_prefix` to `t_stage_prefix` & MX=-1 commit e68141f Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 17:41:33 2025 +0200 remove MX (-1), as it is not valid TNM stage commit ddd65ea Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 11:05:57 2025 +0200 rename `dist_mid` to `dist_to_midline` commit fc7c60d Author: Roman Ludwig <[email protected]> Date: Thu Aug 21 09:55:37 2025 +0200 rm ukf.docx commit 292628a Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 14:30:04 2025 +0200 rm empty UKF cols & document follo-up/recurrence commit 0c3b448 Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 14:14:56 2025 +0200 add metainfor to UKF dataset commit c1be95a Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 12:55:35 2025 +0200 shift 2025-USZ dates randomly commit ad0ab7b Author: Roman Ludwig <[email protected]> Date: Wed Aug 20 10:44:20 2025 +0200 fix location of two 2025 USZ patients commit de48e8a Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 17:02:07 2025 +0200 add hypo/larynx are plots to figures folders commit 8ca7503 Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 15:50:08 2025 +0200 add (unused) script to infer location from ICD commit c11011a Author: Roman Ludwig <[email protected]> Date: Tue Aug 19 11:28:55 2025 +0200 fine-tune area plot commit af0016d Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 17:15:03 2025 +0200 make first version of subsite/T-stage plot commit 66daff5 Merge: ab04379 ea9d4b5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 13:55:43 2025 +0200 Merge branch '23-unique-ids' into dev commit ea9d4b5 Author: Roman Ludwig <[email protected]> Date: Mon Aug 18 13:22:45 2025 +0200 add N-stage suffix to 2025-usz Also, for some patients typos were corrected. Thus, one more patient is now in the table because their ICD code was corrected. commit 6c56a63 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 17:38:56 2025 +0200 don't use -1 for MX stage, but simply `None` commit 4b519c6 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 14:09:34 2025 +0200 add unique IDs to every row Fixes: #23 commit c5993c1 Merge: ab04379 f622116 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 10:04:42 2025 +0200 Merge branch '21-change-2nd-level-headers' into dev commit f622116 Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 10:00:05 2025 +0200 make every cmd use its own set of dependencies commit 08fd2bc Author: Roman Ludwig <[email protected]> Date: Wed Aug 6 09:33:34 2025 +0200 change docs about midlvl cols to "core" commit fb55afa Author: Roman Ludwig <[email protected]> Date: Thu Jul 31 14:44:51 2025 +0200 start changing midlvl cols to "core" Some scripts aren't working yet, though. Related: #21 commit 099f4e3 Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 16:33:11 2025 +0200 add info on UKF data & reproducing pipeline commit 83654ae Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 16:14:04 2025 +0200 make scripts' deps independent using uv commit 5a96af5 Merge: c44bef4 b0456ba Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 15:08:29 2025 +0200 pin numpy dependency commit b0456ba Author: Roman Ludwig <[email protected]> Date: Wed Jul 30 15:02:55 2025 +0200 pin numpy dependency commit c44bef4 Author: Roman Ludwig <[email protected]> Date: Fri Jul 25 11:14:06 2025 +0200 update/improve UMCG/USZ column description commit d3b511b Author: Roman Ludwig <[email protected]> Date: Wed Jul 23 08:51:45 2025 +0200 update & refactor scripts, rerun pipeline commit 894cbe1 Author: Roman Ludwig <[email protected]> Date: Tue Jul 22 17:22:36 2025 +0200 update scripts & rerun with new lyscripts commit ce2ac25 Author: Roman Ludwig <[email protected]> Date: Tue Jul 22 11:31:55 2025 +0200 rerun pipeline (figures not yet working) commit 25d04f7 Author: Roman Ludwig <[email protected]> Date: Mon Jul 21 16:43:32 2025 +0200 replace `#` and `1` with `info` in 2nd lvl headers commit ab04379 Author: Roman Ludwig <[email protected]> Date: Mon Jul 21 13:42:07 2025 +0200 generate figures for 2025-usz-... too commit fe439c2 Merge: 325b469 fbf73af Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 14:08:42 2025 +0200 merge: branch '2025-usz-hypopharynx-larynx' into 'dev' commit 325b469 Merge: 819d83f a98137c Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 13:32:54 2025 +0200 merge: branch '2025-umcg-hypopharynx-larynx' into 'dev' commit fbf73af Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 11:37:41 2025 +0200 add/update README(s) commit 8015cf3 Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 10:40:50 2025 +0200 add/update CITATION.cff commit 60a4723 Author: Roman Ludwig <[email protected]> Date: Fri Jul 18 10:38:00 2025 +0200 add CITATION.cff validation as pre-commit hooks commit c2eca36 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 11:24:24 2025 +0200 add IDs to table and make pipeline work again commit a98137c Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:24:31 2025 +0200 add citations file to UMCG dataset commit 819d83f Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:15:41 2025 +0200 Revert "move licenses" This reverts commit f7a6ae3. commit f7a6ae3 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:15:01 2025 +0200 move licenses commit 61e456d Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 10:13:57 2025 +0200 improve legal framework commit 5b36333 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 09:48:30 2025 +0200 small fix in readme templates commit 7fd4c65 Author: Roman Ludwig <[email protected]> Date: Thu Jul 17 09:30:34 2025 +0200 update readme & reorder pipeline commit 6da1d4e Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 15:57:00 2025 +0200 refactor scripts and update DVC configuration - update DVC to use latest lyscripts - update UMCG to new file path under 2025-... - remove unnecessary stages - add rendering of UMCG data README - refactor Python scripts commit fa163cb Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 15:40:13 2025 +0200 stop tracking 2025-umcg-hypopharynx-larynx/README.md commit 2c94f73 Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 13:56:24 2025 +0200 rename hypopharynx-larynx USZ data to 2025 commit 60651e6 Author: Roman Ludwig <[email protected]> Date: Wed Jul 16 12:50:50 2025 +0200 rename UMCG data to 2025 commit c15b908 Author: Roman Ludwig <[email protected]> Date: Tue Jul 8 18:28:44 2025 +0200 add contributing guide Related: #22 commit 60cc9f0 Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 15:03:36 2025 +0200 reduce unnecessary pipeline steps & rerun commit 0b03802 Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 15:00:51 2025 +0200 recompile Python requirements & rerun pipeline commit 5049dad Author: Roman Ludwig <[email protected]> Date: Fri Jun 27 14:57:05 2025 +0200 remove library and related files/config The library now lives in its own dedicated repo and there is no need anymore to track it here. Fixes: #20 commit d8cdb38 Author: Roman Ludwig <[email protected]> Date: Tue Jun 24 16:03:25 2025 +0200 fix: broken lyscripts docs links commit 340753e Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 14:46:37 2025 +0200 chore: update links after transfer to lycosystem commit 5876fd2 Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 13:41:41 2025 +0200 ci: rename README.template to README.md.jinja commit 85a28f0 Author: Roman Ludwig <[email protected]> Date: Wed Jun 18 11:36:41 2025 +0200 chore: update pre-commit & ruff rules commit abc9236 Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:53:43 2025 +0100 fix missing age in last patient commit c2e87a0 Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:50:40 2025 +0100 fix missing subsite in one patient This particular patient was double checked with the people from Freiburg. commit 2f9b6fb Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:48:37 2025 +0100 add missing M0 stage for two patients commit bab314e Author: Roman Ludwig <[email protected]> Date: Mon Feb 17 15:25:40 2025 +0100 add 'c' prefix to T-stage All patients where at least clinically staged, so they must all have at least a 'c' as T-stage prefix. commit 61ad709 Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 11:48:36 2025 +0100 add conflicts to pipeline commit bf0a1cd Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 11:48:14 2025 +0100 add script to plot conflicts btw modalities commit 467e856 Author: Roman Ludwig <[email protected]> Date: Tue Feb 4 09:43:51 2025 +0100 rename `FNA` to `sonography` In a call with Dr. Rühle, he mentioned that they used `FNA` to encode a sonography diagnosis. So, we renamed that. commit 15ff90e Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:29:07 2025 +0100 remove another weird quote string commit cb605d4 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:26:32 2025 +0100 replace id with institution name commit 3841e8e Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 14:02:28 2025 +0100 reorder & add id nums to data.csv I applied the following commands in order: ```bash lyscripts data join --inputs ruehle.csv schaefer.csv --output joined.csv nl -b p'^,' joined.csv > numbered.csv sed 's/^[[:space:]]*\([0-9]*\)[[:space:]]*/\1/' numbered.csv > data.csv ``` commit c8de9a1 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 13:48:28 2025 +0100 concat & add id nums to ruehle & schaefer commit 9eecdfb Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:41:17 2025 +0100 make central true if position is central commit 5df4944 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:39:21 2025 +0100 remove weird string of quotes from schafer.csv commit 1db3aa8 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:37:54 2025 +0100 fix T-stage prefix and 'ambiguous' position commit 0daa185 Author: Roman Ludwig <[email protected]> Date: Thu Jan 16 12:34:39 2025 +0100 fix negative age in one patient commit ce4ee5b Author: Roman Ludwig <[email protected]> Date: Wed Jan 15 17:09:15 2025 +0100 add parsed CSV files from Freiburg (UKF) commit 3412f8e Author: Roman Ludwig <[email protected]> Date: Thu Apr 4 09:54:42 2024 +0200 rerun pipeline (no changes?) commit 0fb37bf Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 12:24:07 2024 +0200 add follow-up & recurrene info commit 167e6e0 Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 11:26:03 2024 +0200 fix wrong regional recurrence in one patient commit 9d95484 Author: Roman Ludwig <[email protected]> Date: Wed Apr 3 11:00:20 2024 +0200 add distance to midline commit 63c9d1b Author: Roman Ludwig <[email protected]> Date: Mon Mar 25 16:51:21 2024 +0100 rerun pipeline commit 91fd97f Author: Roman Ludwig <[email protected]> Date: Mon Mar 25 16:45:46 2024 +0100 del C10.8 patient & change C12.9 to C12 commit 093a1a4 Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 15:22:15 2024 +0100 fix smoking & T-cat, create plots commit ff5d4ea Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 14:52:18 2024 +0100 join surgery & radiotherapy data commit b12fc36 Author: Roman Ludwig <[email protected]> Date: Mon Mar 18 14:38:34 2024 +0100 add LNL VII to surgery patients commit 66147fc Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:49:04 2024 +0100 rerun after merge commit af74a3a Merge: a4b4210 258ce1a Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:47:55 2024 +0100 Merge branch 'tmp' into 2024-umcg-hypopharynx-larynx commit 258ce1a Author: Roman Ludwig <[email protected]> Date: Fri Mar 15 17:47:17 2024 +0100 join UMCG datasets & rerun pipeline commit a4b4210 Author: rmnldwg <[email protected]> Date: Wed Feb 21 14:22:02 2024 +0100 add LNL VII to radiotherapy patients commit 52a35f5 Author: Roman Ludwig <[email protected]> Date: Tue Feb 20 09:56:55 2024 +0100 create first version of mapping of surgical data commit 56bd28a Author: rmnldwg <[email protected]> Date: Wed Feb 14 17:33:03 2024 +0100 choose earliest of dates & set unknown age to -1 commit eadff41 Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:30:22 2024 +0100 fix all True involvement commit b723519 Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:16:16 2024 +0100 fix mixxing age commit 710a34a Author: rmnldwg <[email protected]> Date: Wed Feb 14 15:12:20 2024 +0100 add lower bound to lyscripts commit 24983ad Author: rmnldwg <[email protected]> Date: Wed Feb 14 14:50:39 2024 +0100 first successful tranformation of rad data commit c036695 Author: Roman Ludwig <[email protected]> Date: Wed Feb 14 10:46:51 2024 +0100 start writing mapping for UMCG dataset commit caecfc6 Author: Roman Ludwig <[email protected]> Date: Tue Feb 13 13:53:17 2024 +0100 update midline extension info in radiotherapy data commit b657af1 Author: rmnldwg <[email protected]> Date: Mon Feb 12 17:32:04 2024 +0100 add raw data from UMCG commit 843a895 Author: rmnldwg <[email protected]> Date: Tue Nov 21 11:06:32 2023 +0100 add id, insititution to hypo/larynx data via stage commit 23098ee Merge: c407abd 304d985 Author: rmnldwg <[email protected]> Date: Tue Nov 21 11:05:04 2023 +0100 merge: branch 'main' into '2023-usz-hypopharynx-larynx' commit c407abd Merge: 0cd41e4 29221aa Author: rmnldwg <[email protected]> Date: Tue Nov 21 09:38:52 2023 +0100 merge: branch 'main' into '2023-usz-hypopharynx-larynx' commit 0cd41e4 Author: rmnldwg <[email protected]> Date: Fri Oct 20 12:59:49 2023 +0800 fix pCT date & add consensus to patients commit 5c3d19a Author: rmnldwg <[email protected]> Date: Fri Oct 20 11:53:25 2023 +0800 create data.csv from raw parsed.csv commit 7b97ac8 Author: rmnldwg <[email protected]> Date: Thu Oct 19 13:36:20 2023 +0800 change "ambiguous" to "central" in tumor side commit 6e2575d Author: rmnldwg <[email protected]> Date: Tue Oct 17 16:20:15 2023 +0800 add parsed CSV data table
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