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add declump tests following pyDeClump doc #932

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add declump tests following pyDeClump doc #932

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62d2f99
Fix interal hyperlink in installation.rst
zacsimile Mar 4, 2021
0c560b0
add declump tests following pyDeClump doc
barentine Mar 6, 2021
f58a28a
add tests for c version
barentine Mar 7, 2021
553c726
fix localization setting url
barentine Mar 7, 2021
48cccd7
Merge pull request #938 from barentine/uiloc
David-Baddeley Mar 8, 2021
c8d04ba
Merge pull request #924 from zacsimile/hyperlink-removal
David-Baddeley Mar 8, 2021
f9a4ba6
Merge branch 'declumptest' of https://github.com/barentine/python-mic…
barentine Mar 8, 2021
968baa7
fix len issue
barentine Mar 8, 2021
2e1e96f
clarify test names and align tests with intention
barentine Mar 8, 2021
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2 changes: 1 addition & 1 deletion PYME/cluster/clusterUI/clusterbrowser/templates/clusterbrowser/dirlisting.html
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Expand Up @@ -209,7 +209,7 @@ <h1>Listing of /{% for bc in breadcrumbs %}<a href="/files/{{ bc.path }}">{{ bc.
function on_analysis_settings(fitModule='LatGaussFitFR'){
//console.log('about to reload')
togglePanel('#localization_form');
$('#localization_form').load('/localization/settings/' + fitModule,function () {
$('#localization_form').load('/localization/settings/' + fitModule + '/', function () {
//alert( "Load was performed." );
// $(this).unwrap();
//console.log('load performed')
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2 changes: 1 addition & 1 deletion docs/Installation/Installation.rst
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Expand Up @@ -5,7 +5,7 @@ Installation

The best PYME installation method will depend on your background and whether you are already using python on your computer.

If you have an existing PYME installation, we recommend :ref:`removing it<Removing a PYME install>` before installing a new one.
If you have an existing PYME installation, we recommend :ref:`removing it<Removing a PYME install>`_ before installing a new one.

Executable installers (Windows and OSX)
=======================================
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46 changes: 45 additions & 1 deletion tests/PYME/Analysis/points/test_clumps.py
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Expand Up @@ -40,4 +40,48 @@ def test_coalesce_incomplete_nontrivial():
x = np.random.rand(len(assigned))
x_out = multiview.coalesce_dict_sorted({'x': x}, assigned, ['x', ], {}, discard_trivial=True)['x']

assert len(x_out) == len(np.unique(assigned[assigned >= 1]))
assert len(x_out) == len(np.unique(assigned[assigned >= 1]))

def test_pydeclump_findclumps_gap():
from PYME.Analysis.points.DeClump import pyDeClump
import numpy as np
x = np.array([0, 0, 0])
y = x
t = np.array([0, 1, 3], dtype=np.int32)
dist = 2 * np.ones(len(x))
assigned = pyDeClump.findClumps(t.astype(np.int32), x, y, dist, 1)
# should group all points as there is only a 1 frame gap
np.testing.assert_array_equal([1, 1, 1], assigned)

def test_declump_findclumps_gap():
from PYME.Analysis.points.DeClump import deClump
import numpy as np
x = np.array([0, 0, 0])
y = x
t = np.array([0, 1, 3], dtype=np.int32)
dist = 2 * np.ones(len(x))
assigned = deClump.findClumps(t.astype(np.int32), x.astype(np.float32), y.astype(np.float32), dist.astype(np.float32), 1)
# should group all points as there is only a 1 frame gap
np.testing.assert_array_equal([1, 1, 1], assigned)

def test_pydeclump_findclumps_same_frame():
from PYME.Analysis.points.DeClump import pyDeClump
import numpy as np
x = np.array([0, 0])
y = x
t = np.array([0, 0], dtype=np.int32)
dist = 2 * np.ones(2)
assigned = pyDeClump.findClumps(t.astype(np.int32), x, y, dist, 0)
# should not group any points because they are both on the same frame
np.testing.assert_array_equal([1, 2], assigned)

def test_declump_findclumps_same_frame():
from PYME.Analysis.points.DeClump import deClump
import numpy as np
x = np.array([0, 0])
y = x
t = np.array([0, 0], dtype=np.int32)
dist = 2 * np.ones(len(x))
assigned = deClump.findClumps(t.astype(np.int32), x.astype(np.float32), y.astype(np.float32), dist.astype(np.float32), 0)
# should not group any points because they are both on the same frame
np.testing.assert_array_equal([1, 2], assigned)