make the recarray viewer also handle tabular data (and add save) by David-Baddeley · Pull Request #624 · python-microscopy/python-microscopy

David-Baddeley · 2020-11-21T10:02:23Z

Addresses issue #584.

Proposed changes:

Makes the existing recarray view handle tabular data as well and adds a save button.

currently implemented as a drop in replacement for the couple of recarray views
launchable by clicking on a tabular item in the pipeline

TODOs:

launch / add tab automatically for certain analyses
integrate plotting and potentially sorting from New module for visualizing pipeline data in a table #594
a bit laggy for full localisation data.

github-actions

Lintly has detected code quality issues in this pull request.

codecov · 2020-11-21T10:08:53Z

Codecov Report

Merging #624 (bf6cae3) into master (2e4edb9) will decrease coverage by 0.01%.
The diff coverage is 1.69%.

@@            Coverage Diff            @@
##           master    #624      +/-   ##
=========================================
- Coverage    8.29%   8.27%   -0.02%     
=========================================
  Files         848     849       +1     
  Lines       97595   97989     +394     
=========================================
+ Hits         8093    8110      +17     
- Misses      89502   89879     +377

Impacted Files	Coverage Δ
PYME/DSView/modules/blobFinding.py	`0.00% <0.00%> (ø)`
PYME/LMVis/triBlobs.py	`2.29% <0.00%> (ø)`
PYME/recipes/recipeGui.py	`0.00% <0.00%> (ø)`
PYME/ui/recArrayView.py	`0.00% <0.00%> (ø)`
PYME/IO/tabular.py	`55.71% <9.09%> (-0.94%)`	⬇️
PYME/config.py	`46.80% <0.00%> (-9.83%)`	⬇️
PYME/Acquire/Hardware/Camera.py	`30.14% <0.00%> (-0.38%)`	⬇️
PYME/LMVis/VisGUI.py	`0.00% <0.00%> (ø)`
PYME/LMVis/visCore.py	`0.00% <0.00%> (ø)`
PYME/Acquire/Spooler.py	`71.90% <0.00%> (ø)`
... and 15 more

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zacsimile · 2020-11-21T15:36:31Z

I gave it a whirl. Pretty cool! A few thoughts.

The title should read Data table - <Data Source Name>. This is especially important if you launch more than one of these views at a time.
The window that pops up is too large. Need to drag around a bit to resize, kind of inconvenient.
Save should default to .csv, as I think this is the more common use case. You can already save to .hdf from the File menu.
I wish I could click on the line in between tiles (and the area between the line and the data source name) to launch the tabular view. It's slightly annoying to have to double-click just on the data source name only, and I think this will make this feature less discoverable. A bigger target would be helpful.
It would be nice if this worked on the Data pipeline view down the left side of the viewing window.
A bit weird that the values all appear editable, but clearly are not
Clicking on a column to sort would be nice

github-actions

Lintly has detected code quality issues in this pull request.

github-actions

Lintly has detected code quality issues in this pull request.

David-Baddeley · 2020-11-22T21:52:23Z

Save should default to .csv, as I think this is the more common use case. You can already save to .hdf from the File menu.
Might arguably be the more common at present, but I'd like, e.g. a save results, open in jupyter workflow to become more common. HDF saving is going to give you much better performance (both saving and opening again) and is probably the best option if you are using either jupyter or matlab for subsequent processing, .csv is the excel fallback. Note that most use cases do not currently have any saving available from the menu.

I wish I could click on the line in between tiles (and the area between the line and the data source name) to launch the tabular view. It's slightly annoying to have to double-click just on the data source name only, and I think this will make this feature less discoverable. A bigger target would be helpful.
Should only need a single-click on the label. Could look at making lines clickable too, but might be a decent bit of work (and hard to maintain across different recipe viewers). Ultimately clicking on a label in the recipe is a somewhat secondary use case - we'd ideally pop this up or add as a tab whenever we generate results that it makes sense for the user to see (e.g. Analysis-->Measure objects should pop up one of these with the results. I.E discoverability should be less of an issue.

It would be nice if this worked on the Data pipeline view down the left side of the viewing window.
A bit weird that the values all appear editable, but clearly are not
Will call these two lowish priority for now.

Clicking on a column to sort would be nice
Needs some form of caching for acceptable performance (and a way of sorting the row labels). Punting until we integrate more of #594

github-actions

Lintly has detected code quality issues in this pull request.

github-actions · 2020-11-22T22:21:41Z

+        bSave = wx.BitmapButton(self, -1, wx.ArtProvider.GetBitmap(wx.ART_FILE_SAVE), style=wx.NO_BORDER | wx.BU_AUTODRAW, name='Save')
+        bSave.Bind(wx.EVT_BUTTON, self.OnSave)
+        tool_sizer.Add(bSave)
+


W293: blank line contains whitespace

github-actions · 2020-11-22T22:21:42Z

+        sizer = wx.BoxSizer(wx.VERTICAL)
+
+        tool_sizer = wx.BoxSizer(wx.HORIZONTAL)
+        bSave = wx.BitmapButton(self, -1, wx.ArtProvider.GetBitmap(wx.ART_FILE_SAVE), style=wx.NO_BORDER | wx.BU_AUTODRAW, name='Save')


E501: line too long (135 > 130 characters)

github-actions · 2020-11-22T22:21:42Z


-        self.grid = RecarrayTableGrid(self, recarray)
+        sizer = wx.BoxSizer(wx.VERTICAL)
+


W293: blank line contains whitespace

github-actions · 2020-11-22T22:21:42Z

+class ArrayTableGrid(gridlib.Grid):
+    def __init__(self, parent, data):
+        gridlib.Grid.__init__(self, parent, -1, size = (-1,-1))
+


W293: blank line contains whitespace

github-actions · 2020-11-22T22:21:42Z

+
+class ArrayTableGrid(gridlib.Grid):
+    def __init__(self, parent, data):
+        gridlib.Grid.__init__(self, parent, -1, size = (-1,-1))


E231: missing whitespace after ','

github-actions · 2020-11-22T22:21:42Z

+
+class ArrayTableGrid(gridlib.Grid):
+    def __init__(self, parent, data):
+        gridlib.Grid.__init__(self, parent, -1, size = (-1,-1))


E251: unexpected spaces around keyword / parameter equals

github-actions · 2020-11-22T22:21:42Z


    def GetValue(self, row, col):
-        return str( self.recarray[row][col] )
+        return str(self.recarray[row][col] )


E202: whitespace before ')'

github-actions · 2020-11-22T22:21:42Z

 import wx
-import  wx.grid as  gridlib
+import wx.grid as gridlib
+import numpy as np


F401: 'numpy as np' imported but unused

github-actions · 2020-11-22T22:21:43Z

                        mode = 'lite'

                    dv = ViewIm3D(outp, mode=mode, glCanvas=self.recipes.dsviewer.glCanvas)
+


W293: blank line contains whitespace

github-actions · 2020-11-22T22:21:43Z



-            vObjFit = recArrayView.recArrayPanel(self.dsviewer, self.objFitRes[chnum]['fitResults'])
+            vObjFit = recArrayView.ArrayPanel(self.dsviewer, self.objFitRes[chnum]['fitResults'])


E303: too many blank lines (2)

make the recarray viewer also handle tabular data (and add save)

1f9617a

github-actions Bot requested changes Nov 21, 2020

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David-Baddeley mentioned this pull request Nov 22, 2020

[BUG] Measure objects has prominent placement but it's unclear how to use it #613

Closed

fix array view default size and title

b83869a

github-actions Bot requested changes Nov 22, 2020

View reviewed changes

some lint fixes

42e2f07

github-actions Bot requested changes Nov 22, 2020

View reviewed changes

add simple caching

bf6cae3

github-actions Bot requested changes Nov 22, 2020

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David-Baddeley mentioned this pull request Nov 22, 2020

[ENHANCEMENT] Make it easier to visualize and export measurements from PYMEVis #584

Open

David-Baddeley merged commit 6ea2dc4 into python-microscopy:master Nov 22, 2020

David-Baddeley deleted the recarray-view-tweaks branch January 25, 2021 21:25


		self.grid = RecarrayTableGrid(self, recarray)
		sizer = wx.BoxSizer(wx.VERTICAL)

		mode = 'lite'

		dv = ViewIm3D(outp, mode=mode, glCanvas=self.recipes.dsviewer.glCanvas)



		vObjFit = recArrayView.recArrayPanel(self.dsviewer, self.objFitRes[chnum]['fitResults'])
		vObjFit = recArrayView.ArrayPanel(self.dsviewer, self.objFitRes[chnum]['fitResults'])

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