Conversion between pixel_mask and image_mask #766

mamelara · 2018-12-18T00:27:43Z

Motivation

Addresses Issue #669

How to test the behavior?

Unit tests are included. To run the tests, use tox.

Checklist

Have you checked our Contributing document?
Have you ensured the PR description clearly describes problem and the solution?
Is your contribution compliant with our coding style ? This can be checked running flake8 from the source directory.
Have you checked to ensure that there aren't other open Pull Requests for the same change?
Have you included the relevant issue number using #XXX notation where XXX is the issue number ?

mamelara · 2018-12-18T00:28:25Z

This is still WIP, but just wanted to see if I'm going in the right direction with this. I also need to take into account that an image_mask can have multiple image matrices in it.

oruebel · 2018-12-18T00:48:08Z

src/pynwb/ophys.py

@@ -271,6 +271,27 @@ def add_roi(self, **kwargs):
            rkwargs['voxel_mask'] = voxel_mask
        return super(PlaneSegmentation, self).add_row(**rkwargs)

+    def pixel_to_image(self, pixel_mask, width, height):
+        image_matrix = np.zeros((width, height))
+        for mask in pixel_mask:


I think something like this might be a bit faster than setting all the elements one-by-one in the for loop:

npmask = np.asarray(pixel_mask) image_matrix[npmask[:,0], npmask[:,1]] = npmask[:,-1] return image_matrix

oruebel · 2018-12-18T01:07:34Z

src/pynwb/ophys.py

+
+    def image_to_pixel(self, image_mask):
+        """Convert a image_mask to a pixel_mask that contains all the elements of the form (x, y, weight)"""
+        width, height = np.shape(image_mask)


Here numpy nditer might help simplify things:

pixel_mask = [] it = np.nditer(image_mask, flags=['multi_index']) while not it.finished: pixel_mask.append( [it.multi_index[0], it.multi_index[1], it[0][()]] ) it.iternext() return pixel_mask

codecov · 2018-12-21T06:44:27Z

Codecov Report

Merging #766 into dev will increase coverage by 0.04%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##              dev     #766      +/-   ##
==========================================
+ Coverage   74.63%   74.68%   +0.04%     
==========================================
  Files          60       60              
  Lines        6932     6963      +31     
  Branches     1450     1457       +7     
==========================================
+ Hits         5174     5200      +26     
  Misses       1353     1353              
- Partials      405      410       +5

Impacted Files	Coverage Δ
src/pynwb/ophys.py	`95.41% <100%> (+0.77%)`	⬆️
src/pynwb/form/utils.py	`87.2% <0%> (-0.59%)`	⬇️
src/pynwb/file.py	`79.66% <0%> (-0.52%)`	⬇️
src/pynwb/misc.py	`92.55% <0%> (-0.48%)`	⬇️

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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codecov · 2018-12-21T06:44:27Z

Codecov Report

Merging #766 into dev will increase coverage by 0.04%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##              dev     #766      +/-   ##
==========================================
+ Coverage   74.63%   74.68%   +0.04%     
==========================================
  Files          60       60              
  Lines        6932     6963      +31     
  Branches     1450     1457       +7     
==========================================
+ Hits         5174     5200      +26     
  Misses       1353     1353              
- Partials      405      410       +5

Impacted Files	Coverage Δ
src/pynwb/ophys.py	`95.41% <100%> (+0.77%)`	⬆️
src/pynwb/form/utils.py	`87.2% <0%> (-0.59%)`	⬇️
src/pynwb/file.py	`79.66% <0%> (-0.52%)`	⬇️
src/pynwb/misc.py	`92.55% <0%> (-0.48%)`	⬇️

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update d8fb82a...6a6843e. Read the comment docs.

codecov · 2018-12-21T06:44:27Z

Codecov Report

Merging #766 into dev will increase coverage by 1.6%.
The diff coverage is 100%.

@@            Coverage Diff            @@
##              dev     #766     +/-   ##
=========================================
+ Coverage   73.07%   74.68%   +1.6%     
=========================================
  Files          36       60     +24     
  Lines        2715     6963   +4248     
  Branches      521     1457    +936     
=========================================
+ Hits         1984     5200   +3216     
- Misses        615     1353    +738     
- Partials      116      410    +294

Impacted Files	Coverage Δ
src/pynwb/ophys.py	`95.41% <100%> (+1.4%)`	⬆️
src/pynwb/epoch.py	`73.13% <0%> (-9.22%)`	⬇️
src/pynwb/core.py	`70.6% <0%> (-3.15%)`	⬇️
src/pynwb/__init__.py	`69.49% <0%> (-2.55%)`	⬇️
src/pynwb/icephys.py	`88.88% <0%> (-0.4%)`	⬇️
src/pynwb/ecephys.py	`97.29% <0%> (-0.08%)`	⬇️
src/pynwb/ogen.py	`100% <0%> (ø)`	⬆️
src/pynwb/behavior.py	`100% <0%> (ø)`	⬆️
src/pynwb/validate.py	`0% <0%> (ø)`	⬆️
src/pynwb/retinotopy.py	`100% <0%> (ø)`	⬆️
... and 33 more

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Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 1acfa8f...6f4f634. Read the comment docs.

src/pynwb/ophys.py

bendichter · 2018-12-29T00:33:33Z

src/pynwb/ophys.py

@@ -272,6 +272,27 @@ def add_roi(self, **kwargs):
            rkwargs['voxel_mask'] = voxel_mask
        return super(PlaneSegmentation, self).add_row(**rkwargs)

+    def pixel_to_image(self, pixel_mask):


Suggested change

def pixel_to_image(self, pixel_mask):

def pixel_to_image(pixel_mask):

src/pynwb/ophys.py

bendichter · 2018-12-29T00:34:00Z

src/pynwb/ophys.py

+        image_matrix[y_coords, x_coords] = weights
+        return image_matrix
+
+    def image_to_pixel(self, image_mask):


Suggested change

def image_to_pixel(self, image_mask):

def image_to_pixel(image_mask):

bendichter · 2018-12-29T00:34:17Z

src/pynwb/ophys.py

+    def pixel_to_image(self, pixel_mask):
+        image_matrix = np.zeros(np.shape(pixel_mask))
+        npmask = np.asarray(pixel_mask)
+        x_coords = tuple(map(int, npmask[:, 0]))


Suggested change

x_coords = tuple(map(int, npmask[:, 0]))

x_coords = npmask[:, 0].astype(np.int)

bendichter · 2018-12-29T00:34:32Z

src/pynwb/ophys.py

+        image_matrix = np.zeros(np.shape(pixel_mask))
+        npmask = np.asarray(pixel_mask)
+        x_coords = tuple(map(int, npmask[:, 0]))
+        y_coords = tuple(map(int, npmask[:, 1]))


Suggested change

y_coords = tuple(map(int, npmask[:, 1]))

y_coords = npmask[:, 1].astype(np.int)

oruebel · 2019-07-31T00:19:07Z

@mamelara what is the status of this PR? Looks like there were a few minor changes requested, could you add those so we can close and merge?

Work in progress for creating methods that convert pixel to image and image to pixel mask. Eventually, will need to handle image masks that have multiple image matrices.

Uses numpy's way of indexing and iterating over numpy arrays to create images and pixels.

Modify some of the tests and also add a helper function for creating a basic plane segmentation when the boiler plate objects are not needed for testing

Suggestions include making pixel_to_image and image_to_pixel as staticmethods and using np.mask rather than tuples.

mamelara · 2019-07-31T21:21:09Z

Rebased to current dev and added suggested changes

oruebel

It would be good to add a brief docstring to the pixel_to_image and image_to_pixel methods to describe what they do, but other than that I think this looks good.

oruebel reviewed Dec 18, 2018

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bendichter reviewed Dec 29, 2018

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bendichter reviewed Dec 29, 2018

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bendichter reviewed Dec 29, 2018

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mamelara changed the title ~~WIP: Conversion between pixel_mask and image_mask~~ Conversion between pixel_mask and image_mask Jan 10, 2019

mamelara added 6 commits July 31, 2019 14:19

Add methods that convert pixel to image and vice versa

dee08f0

Work in progress for creating methods that convert pixel to image and image to pixel mask. Eventually, will need to handle image masks that have multiple image matrices.

Add tests for masks conversion

ca01a69

Refactor conversion methods

c05b226

Uses numpy's way of indexing and iterating over numpy arrays to create images and pixels.

Rename tests and create helper method

b2cea11

Modify some of the tests and also add a helper function for creating a basic plane segmentation when the boiler plate objects are not needed for testing

Flake8 fixes

55fb3ab

Add suggested changes

c335433

Suggestions include making pixel_to_image and image_to_pixel as staticmethods and using np.mask rather than tuples.

mamelara force-pushed the mask_conversion branch from 888b76f to c335433 Compare July 31, 2019 21:20

oruebel previously approved these changes Jul 31, 2019

View reviewed changes

Add docstring

6f4f634

mamelara dismissed oruebel’s stale review via 6f4f634 July 31, 2019 21:55

oruebel approved these changes Jul 31, 2019

View reviewed changes

oruebel merged commit 8b010af into NeurodataWithoutBorders:dev Jul 31, 2019

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Conversion between pixel_mask and image_mask #766

Conversion between pixel_mask and image_mask #766

mamelara commented Dec 18, 2018 •

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mamelara commented Dec 18, 2018

oruebel Dec 18, 2018

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bendichter Dec 29, 2018

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oruebel commented Jul 31, 2019

mamelara commented Jul 31, 2019

oruebel left a comment

	def pixel_to_image(self, pixel_mask):
	def pixel_to_image(pixel_mask):

	def image_to_pixel(self, image_mask):
	def image_to_pixel(image_mask):

	x_coords = tuple(map(int, npmask[:, 0]))
	x_coords = npmask[:, 0].astype(np.int)

	y_coords = tuple(map(int, npmask[:, 1]))
	y_coords = npmask[:, 1].astype(np.int)

Conversion between pixel_mask and image_mask #766

Conversion between pixel_mask and image_mask #766

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mamelara commented Dec 18, 2018 • edited Loading

Motivation

How to test the behavior?

Checklist

mamelara commented Dec 18, 2018

oruebel Dec 18, 2018

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oruebel commented Jul 31, 2019

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mamelara commented Dec 18, 2018 •

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