Implement basic label matching #2

jo-mueller · 2021-11-04T07:22:34Z

I implemented functions to match labels based on intersection over union (cpu) that work in 2D and 3D based on cellpose (source)

The functions are biapolutils.label.match_labels and match_labels_stack that rely on label.label_overlap_matrix and label.intersection_over_union.

A basic notebook for label-matching is available.

future versions of these functions should include

a verbose option to track spent time
a GPU accelerated version of IoU calculation. Currently it's relatively slow (~30s for 400x400x50 with ~20 labels) but it works.

for functions see biapolutils.label.match_labels and match_labels_stack

haesleinhuepf

Hi Johannes @jo-mueller ,

great to see this evolving! I just put some comments in the code, mostly asking for better variable naming and some API changes.

Let me know if I can help.

Best,
Robert

haesleinhuepf · 2021-11-04T07:29:05Z

biapolutils/label/_intersection_over_union.py

+def intersection_over_union(masks_true, masks_pred):
+    """ intersection over union of all mask pairs
+
+    From: https://github.com/MouseLand/cellpose/blob/6fddd4da98219195a2d71041fb0e47cc69a4b3a6/cellpose/metrics.py#L165


Can you please make a folder "/license_thirdparty" and put the cellpose license in there? Furthermore, a acknowledgement statment in the readme would be kind.

Added in dee6ee3 and 96e10c6

haesleinhuepf · 2021-11-04T07:29:54Z

biapolutils/label/_label_overlap_matrix.py

+
+import numpy as np
+
+def label_overlap_matrix(x, y):


Can you please rename the variables x and y? I suggest something more descriptive like label_image_x and label_image_y

Added in ab725ce

haesleinhuepf · 2021-11-04T07:31:25Z

biapolutils/label/_match_labels.py

+from skimage import io
+import os
+
+def match_labels_stack(stack, method='iou', **kwargs):


A method should not be passed as string. Please pass the method as method. See this notebook for an example. https://github.com/BiAPoL/Bio-image_Analysis_with_Python/blob/main/python_basics/12_functional_parameters.ipynb

Changed in 92167c9 - Thanks for the source!

haesleinhuepf · 2021-11-04T07:33:02Z

biapolutils/label/_match_labels.py

+
+    return stack
+
+def match_labels(imageA, imageB, method='iou', **kwargs):


please rename imageA and imageB to something more descriptive. Please also be consistent with the naming above, e.g. label_image_x

Also don't pass a method as string like explained above.

Optional arguments changed in 92167c9

haesleinhuepf · 2021-11-04T07:34:14Z

biapolutils/label/_match_labels_3D.py

+import tqdm
+from ._intersection_over_union import intersection_over_union
+
+def stitch3Dto3D(masks, method='iou', **kwargs):


Please rename masks and pass a method, See comments above.

sticht3Dto3D was removed in 31c66f1 - the function is covered by match_labels_stack and works in 2D->3D and 3D->4D.

haesleinhuepf · 2021-11-04T07:35:10Z

main.py

+import matplotlib.pyplot as plt
+
+if __name__=='__main__':
+    path = r'D:\Documents\Promotion\Projects\2021_napari_quantify_segmentation\data\set1_unmatched'


Please replace absolute paths on your computer with relative paths so that this works on all computers. Also please upload the example data. If the dataset is big, I suggest to use a smaller one. I'm personally big fan of example images with size 5x5 pixels.

I added a data submodule with example images that are shipped with biapolutils (ba3c4fb). I couldn't find a license for blobs.gif from ImageJ (source: https://imagej.nih.gov/ij/images/)

blobs is part of ImageJ und thus, public domain :-)
https://imagej.nih.gov/ij/disclaimer.html

haesleinhuepf · 2021-11-04T07:36:15Z

setup.cfg

@@ -31,4 +31,5 @@ install_requires =
    numpy
    scikit-image
    scikit-learn
+    tqdm


As far as I can see, tqdm is not used in your code. Do we really need this dependency? Please also check the other dependencies and reduce them to the absolute minimum

Changed in 3b036f4. I do think, however, that some sort of progress feedback could be valuable in some functions.

haesleinhuepf · 2021-11-04T07:37:56Z

future versions of these functions should include

Also, could you please make individual github issues out of that list? We might otherwise forget to implement that stuff.

Thanks!

…iAPoL/biapol-utilities into implement-basic-label-matching

redundant because implemented in match_labels_stack

haesleinhuepf · 2021-11-04T08:55:57Z

Some more suggestions:

can the main package be called "biapol_utilities"? that would match better to the repository name
remove version from sub-packages such as here
There are manifold versions of the Institute name. Please synchronize to DFG Cluster of Excellence "Physics of Life", TU Dresden.
There are manifold version of the Group name. Please syncronize to Bio-image Analysis Technology Development Group at DFG Cluster of Excellence "Physics of Life", TU Dresden
Remove boiler plate comments from files. E.g. authors here: https://github.com/BiAPoL/biapol-utilities/blob/c2bbfb41e8df894f0be0dbb4d59c50e7d362b752/biapolutils/label/__init__.py Github nicely takes care of who wrote what

added the ImageJ blobs example to biapolutils

use shipped example data for demonstration

haesleinhuepf · 2021-11-04T09:51:54Z

biapol_utilities/__init__.py

@@ -0,0 +1,21 @@
+"""Biapol utilities for Python
+``biapol-utilities`` (a.k.a. ``biapolutils``) is a collection of utility functions


Suggested change

``biapol-utilities`` (a.k.a. ``biapolutils``) is a collection of utility functions

``biapol-utilities`` (a.k.a. ``biapol_utilitiess``) is a collection of utility functions

Changed in 35303e1

haesleinhuepf · 2021-11-04T09:52:10Z

biapol_utilities/__init__.py

+    Label handling and evaluation
+surface
+    Manage surfaces and point representations
+util


Can we please write things out, e.g. "utilities" in this case?

Changed in df73737

haesleinhuepf · 2021-11-04T09:54:42Z

main.py

+import matplotlib.pyplot as plt
+
+if __name__=='__main__':
+    path = r'D:\Documents\Promotion\Projects\2021_napari_quantify_segmentation\data\set1_unmatched'


blobs is part of ImageJ und thus, public domain :-)
https://imagej.nih.gov/ij/disclaimer.html

Updated description

no functions there (yet)

haesleinhuepf · 2021-11-04T15:02:54Z

Hey Johannes @jo-mueller ,

for the future: You should not merge your own pull-request without proper review. Let others be part of the process ;-)

Best,
Robert

jo-mueller added 2 commits November 3, 2021 14:04

added labelmatching in 2D and 3D

d950a66

for functions see biapolutils.label.match_labels and match_labels_stack

added demo notebook for label-matching

80b4b92

jo-mueller requested a review from haesleinhuepf November 4, 2021 07:22

haesleinhuepf requested changes Nov 4, 2021

View reviewed changes

created thirdparty licenses

dee6ee3

haesleinhuepf mentioned this pull request Nov 4, 2021

implement generate_jaccard_index_matrix clEsperanto/pyclesperanto_prototype#138

Open

jo-mueller and others added 5 commits November 4, 2021 08:49

Update README.md

96e10c6

renamed variables

ab725ce

Merge branch 'implement-basic-label-matching' of https://github.com/B…

c2bbfb4

…iAPoL/biapol-utilities into implement-basic-label-matching

Renamed variables

34e57c0

Delete _match_labels_3D.py

31c66f1

redundant because implemented in match_labels_stack

jo-mueller added 8 commits November 4, 2021 10:29

added example data

ba3c4fb

added the ImageJ blobs example to biapolutils

Update match_labels.ipynb

7b46ecd

use shipped example data for demonstration

removed tqdm from requirements

3b036f4

Update __init__.py

e4a00cc

synchronized authorships

8e622e8

renamed main package

35303e1

removed unnecessary comments

296eb6e

updated/synced group names

9286b30

haesleinhuepf reviewed Nov 4, 2021

View reviewed changes

jo-mueller mentioned this pull request Nov 4, 2021

Check if scikit-learn has functions that we can reuse #3

Closed

jo-mueller added 7 commits November 4, 2021 12:15

Create LICENSE_ImageJ

5d797e5

Update _data.py

c1562a4

Updated description

Changed argument type to function

92167c9

added tests

2d21087

removed unnecessary header

f366aab

renamed util -> utilities

df73737

bugfix in tests

92ecbc2

jo-mueller added 2 commits November 4, 2021 13:30

commented import of surface and utilities

2d1e244

no functions there (yet)

bugfix in test

18a843c

jo-mueller merged commit dfd8eac into main Nov 4, 2021

jo-mueller deleted the implement-basic-label-matching branch November 4, 2021 13:18

haesleinhuepf mentioned this pull request Nov 4, 2021

Variable names #10

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Implement basic label matching #2

Implement basic label matching #2

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haesleinhuepf commented Nov 4, 2021


		return stack

		def match_labels(imageA, imageB, method='iou', **kwargs):

		@@ -0,0 +1,21 @@
		"""Biapol utilities for Python
		``biapol-utilities`` (a.k.a. ``biapolutils``) is a collection of utility functions

	``biapol-utilities`` (a.k.a. ``biapolutils``) is a collection of utility functions
	``biapol-utilities`` (a.k.a. ``biapol_utilitiess``) is a collection of utility functions

Implement basic label matching #2

Implement basic label matching #2

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