Updated ghosting function – fixes sampling point issue #185

Lucrezia-Cester · 2021-12-15T18:32:57Z

Hello @laurencejackson, @tomaroberts , I have fixed the ghosting script. The biggest problem was that the ghosting slice was always placed at random points in the image, not where it should have been, namely int the phase encoding direction. There is now a new function called get_ghosting_slice2 which selects the correct ghosting slice. I removed the old get_ghosting_slice function.
I have had to change the code slightly in the main function and in the report_path if statement because it didn't plot correctly.
Finally I changed the rescale_to_byte function because the original one changes the values and spreads them into a more widened histogram. I can put this back how it was but I think ideally that function will need to be changed at some point for all the hazenlib scripts.

@laurencejackson

Hello @laurencejackson, @tomaroberts , I have fixed the ghosting script. The biggest problem was that the ghosting slice was always placed at random points in the image, not where it should have been, namely int the phase encoding direction. There is now a new function called get_ghosting_slice2 which selects the correct ghosting slice. I removed the old get_ghosting_slice function. I have had to change the code slightly in the main function and in the report_path if statement because it didn't plot correctly. Finally I changed the rescale_to_byte function because the original one changes the values and spreads them into a more widened histogram. I can put this back how it was but I think ideally that function will need to be changed at some point for all the hazenlib scripts.

I updated the test_ghosting script to work with the new ghosting function. Now the get_ghost_slice needs to be equal to the eligible area.

github-actions · 2021-12-20T10:22:01Z

Coverage Report

File	Stmts	Miss	Cover	Missing
hazenlib
init.py	129	62	52%	135, 139, 149, 154, 190–193, 198–203, 214, 217–224, 244–246, 264–266, 285–287, 296, 300–303, 307, 313–362
ghosting.py	151	55	64%	24, 89–90, 94, 104–105, 133–135, 151–153, 215–248, 255–275, 280
relaxometry.py	317	90	72%	238–256, 630, 689–691, 745, 793–815, 833–848, 1173–1176, 1185–1188, 1200–1213, 1216–1221, 1233–1263
slice_position.py	110	20	82%	73–74, 99, 183, 190–203, 211, 219–220, 231
slice_width.py	290	45	84%	24, 27, 31, 35–40, 106, 277, 282–283, 289, 294, 357–358, 593–632, 668–671, 674–677
snr.py	165	48	71%	42–47, 75, 209–219, 262–266, 304–315, 321–329, 357–368, 392, 400–402, 405
spatial_resolution.py	295	99	66%	87–145, 159, 251, 291–298, 326, 457–490, 517–534
tools.py	75	6	92%	43–50, 89
uniformity.py	79	22	72%	69–70, 77, 111–123, 135–137, 140, 144–147, 155
TOTAL	1647	447	73%

Tests	Skipped	Failures	Errors	Time
170	0 💤	0 ❌	0 🔥	150.964s ⏱️

Lucrezia-Cester · 2021-12-20T10:24:29Z

Hi @laurencejackson , @tomaroberts I fixed the ghosting script. I also fixed the tests.

Lucrezia-Cester · 2021-12-20T10:27:23Z

I have also fixed the issue which said: prevent ghosting from outputting negative values. That issue is linked. For that I only had to add an absolute value in the ghosting formula. @tomaroberts @laurencejackson

tomaroberts

Thanks for all this Lu – see review comments. Main ones are that the code is always outputting True.png and it would be good to get a bit more clarity on the difference between rescale_to_byte and your version. Thanks!

tomaroberts · 2021-12-20T19:15:43Z

hazenlib/ghosting.py

@@ -223,25 +244,28 @@ def get_ghosting(dcm, plotting=False) -> dict:
        img = cv.rectangle(img.copy(), (x1, y1), (x2, y2), (255, 0, 0), 1)

        ax.imshow(img)
+        fig.savefig(f'{report_path}.png')


When I run hazen ghosting ... --report it outputs a file called True.png. I think it's because you have used report_path here, which = True or False.

On a related note, the function always outputs True.png, even without the --report option. Is that supposed to happen?

tomaroberts · 2021-12-20T19:26:19Z

hazenlib/ghosting.py

    signal_centre = [(bbox[0]+bbox[1])//2, (bbox[2]+bbox[3])//2]
    background_rois = get_background_rois(dcm, signal_centre)
    ghost_col, ghost_row = get_ghost_slice(bbox, dcm, slice_radius=slice_radius)
-    ghost = dcm.pixel_array[(ghost_row, ghost_col)]
+    ghost = dcm.pixel_array[(ghost_col, ghost_row)]


Is this an intentional change, swapping around ghost_col / ghost_row? Just checking in case you left if that way round during testing.

Hi Tom, thank you for all the comments. No, this one is not intentional.

tomaroberts · 2021-12-20T19:33:18Z

hazenlib/ghosting.py

+        img = dcm.pixel_array
+        img = img.astype('float64')
+        #print('this is img',img)
+        img *= 255.0 / img.max()
+        #img = hazenlib.rescale_to_byte(dcm.pixel_array)


The rescale_to_byte function is also used in spatial_resolution.py and possibly others. I'm a little concerned by changing it here and not doing wholesale across the entire repo. What do you think @laurencejackson ?

Lu – can you upload some images of img generated using rescale_to_byte and your new version, to help illustrate how the data differs? I just want to get a better sense of what's changed.

Hi Tom, the original rescale_to_byte function performs an histogram equalisation, which slightly manipulates the data. I think it is unnecessary to manipulate the data when we can just rescale in a more conventional way which does not manipulate the data. However, for this ghosting script, the rescale_to_byte is only used to plot, so actually I would leave the rescale_to_byte original function. I only changed this to check if it was making any difference while trying to fix the ghosting problem.

tomaroberts · 2021-12-20T19:36:56Z

hazenlib/ghosting.py

+    #figures = []
    for dcm in data:
        try:
            key = f"{dcm.SeriesDescription.replace(' ', '_')}_{dcm.EchoTime}ms_NSA-{dcm.NumberOfAverages}"
+            if report_path:
+               report_path = key
        except AttributeError as e:
            print(e)
            key = f"{dcm.SeriesDescription}_{dcm.SeriesNumber}"
        try:
-            fig, results[key] = get_ghosting(dcm, report_path)
-            if report_path:
-                fig.savefig(key + '.png')
+            fig, results[key] = get_ghosting(dcm, report_path=True)
+
+


I don't follow the changes here? Possibly linked to my previous comment about the image True.png being output every time?

Previously I could not get the script to output an image, so that's why I changed it, but now I need to fix this problem of always outputting an image that I created. I'll fix this.

tomaroberts · 2021-12-20T19:38:50Z

tests/test_ghosting.py

+            # assert -5.0 == hazen_ghosting.calculate_ghost_intensity(ghost=np.asarray([5]),
+            #                    phantom=np.asarray([100]),
+        #                   noise=np.asarray([10]))


I think you can remove this – assume your abs() correction has made this redundant.

yes I think so too. Will remove then.

tomaroberts · 2021-12-20T19:41:27Z

tests/test_ghosting.py

        with pytest.raises(Exception):
            hazen_ghosting.calculate_ghost_intensity(ghost=np.asarray([-10]),
-                                                     phantom=np.asarray([-100]),
-                                                     noise=np.asarray([-5]))
+             phantom=np.asarray([-100]),
+         noise=np.asarray([-5]))

        assert 5.0 == hazen_ghosting.calculate_ghost_intensity(ghost=np.asarray([10]),
-                                                               phantom=np.asarray([100]),
-                                                               noise=np.asarray([5]))
+                                               phantom=np.asarray([100]),
+                                        noise=np.asarray([5]))


Some of the indentation in this section is awry – would you mind just tidying.

I'll tidy up the indentation.

tomaroberts · 2021-12-20T19:44:23Z

tests/test_ghosting.py

+        SIGNAL_BOUNDING_BOX = (164, 208, 166, 209)
+        SIGNAL_CENTRE = [186, 187]
+        BACKGROUND_ROIS = [(64, 187), (64, 140), (64, 93), (64, 46)]
+        PADDING_FROM_BOX = 30
+        SLICE_RADIUS = 5
+        ELIGIBLE_GHOST_AREA = range(SIGNAL_BOUNDING_BOX[0], SIGNAL_BOUNDING_BOX[1]), range(
+            SLICE_RADIUS, SIGNAL_BOUNDING_BOX[2] - PADDING_FROM_BOX)
+
+        SIGNAL_SLICE = np.array(range(SIGNAL_CENTRE[0] - SLICE_RADIUS, SIGNAL_CENTRE[0] + SLICE_RADIUS), dtype=np.intp)[
+                       :,
+                       np.newaxis], np.array(range(SIGNAL_CENTRE[1] - SLICE_RADIUS, SIGNAL_CENTRE[1] + SLICE_RADIUS),
+                                             dtype=np.intp)
+        GHOST_SLICE = np.array(
+        range(min(ELIGIBLE_GHOST_AREA[1]), max(ELIGIBLE_GHOST_AREA[1])), dtype=np.intp)[:, np.newaxis], np.array(
+        range(min(ELIGIBLE_GHOST_AREA[0]), max(ELIGIBLE_GHOST_AREA[0]))
+    )
+        PE = "COL"
+        GHOSTING = (None,  0.015138960417776908)

-    def setUp(self):
-        self.file = str(TEST_DATA_DIR / 'ghosting' / 'PE_COL_PHANTOM_BOTTOM_RIGHT' / 'PE_COL_PHANTOM_BOTTOM_RIGHT.IMA')
-        self.dcm = pydicom.read_file(self.file)
+        def setUp(self):
+            self.file = str(
+                TEST_DATA_DIR / 'ghosting' / 'PE_COL_PHANTOM_BOTTOM_RIGHT' / 'PE_COL_PHANTOM_BOTTOM_RIGHT.IMA')
+            self.dcm = pydicom.read_file(self.file)


 class TestAxialPhilipsBroomfields(TestGhosting):
-    SIGNAL_BOUNDING_BOX = (217, 299, 11, 93)
-    SIGNAL_CENTRE = [(SIGNAL_BOUNDING_BOX[0] + SIGNAL_BOUNDING_BOX[1]) // 2,
-                     (SIGNAL_BOUNDING_BOX[2] + SIGNAL_BOUNDING_BOX[3]) // 2]
-    BACKGROUND_ROIS = [(258, 264), (194, 264), (130, 264), (66, 264)]
-    PADDING_FROM_BOX = 30
-    SLICE_RADIUS = 5
-    ELIGIBLE_GHOST_AREA = range(SLICE_RADIUS, SIGNAL_BOUNDING_BOX[0] - PADDING_FROM_BOX), range(
-        SIGNAL_BOUNDING_BOX[2], SIGNAL_BOUNDING_BOX[3])
-    SIGNAL_SLICE = np.array(range(SIGNAL_CENTRE[0] - SLICE_RADIUS, SIGNAL_CENTRE[0] + SLICE_RADIUS), dtype=np.intp)[:,
-                   np.newaxis], np.array(range(SIGNAL_CENTRE[1] - SLICE_RADIUS, SIGNAL_CENTRE[1] + SLICE_RADIUS),
-                                         dtype=np.intp)
-    GHOST_SLICE = np.array(range(11 - SLICE_RADIUS, 11 + SLICE_RADIUS), dtype=np.intp)[:, np.newaxis], np.array(
-        range(16 - SLICE_RADIUS, 16 + SLICE_RADIUS))
+        SIGNAL_BOUNDING_BOX = (217, 299, 11, 93)
+        SIGNAL_CENTRE = [(SIGNAL_BOUNDING_BOX[0] + SIGNAL_BOUNDING_BOX[1]) // 2,
+                         (SIGNAL_BOUNDING_BOX[2] + SIGNAL_BOUNDING_BOX[3]) // 2]
+        BACKGROUND_ROIS = [(258, 264), (194, 264), (130, 264), (66, 264)]
+        PADDING_FROM_BOX = 30
+        SLICE_RADIUS = 5
+        ELIGIBLE_GHOST_AREA = range(SLICE_RADIUS, SIGNAL_BOUNDING_BOX[0] - PADDING_FROM_BOX), range(
+            SIGNAL_BOUNDING_BOX[2], SIGNAL_BOUNDING_BOX[3])
+        SIGNAL_SLICE = np.array(range(SIGNAL_CENTRE[0] - SLICE_RADIUS, SIGNAL_CENTRE[0] + SLICE_RADIUS), dtype=np.intp)[
+                       :,
+                       np.newaxis], np.array(range(SIGNAL_CENTRE[1] - SLICE_RADIUS, SIGNAL_CENTRE[1] + SLICE_RADIUS),
+                                             dtype=np.intp)
+        GHOST_SLICE = np.array(
+        range(min(ELIGIBLE_GHOST_AREA[1]), max(ELIGIBLE_GHOST_AREA[1])), dtype=np.intp)[:, np.newaxis], np.array(
+        range(min(ELIGIBLE_GHOST_AREA[0]), max(ELIGIBLE_GHOST_AREA[0]))
+    )
+
+        GHOSTING = (None,  0.007246960909896829)
+
+        def setUp(self):
+            self.file = str(TEST_DATA_DIR / 'ghosting' / 'GHOSTING' / 'axial_philips_broomfields.dcm')
+            self.dcm = pydicom.read_file(self.file)
+
+
+
+


A lot of this indentation seems to be double-tabbed. Is that intentional? Github thinks the code has changed, but a lot of it looks the same from what I can tell.

I'll tidy up the indentation.

I fixed the problem where the script always outputted an image. Now it should only output if report_path == True

Lucrezia-Cester requested review from tomaroberts and laurencejackson December 15, 2021 18:32

This was linked to issues Dec 15, 2021

Ghosting script does not work for physicists #160

Closed

[HZN-99] Hazen produced ghosting values do not match ImageJ values #99

Closed

[HZN-51] Prevent ghosting from returning negative values #51

Closed

Lucrezia-Cester added 3 commits December 20, 2021 09:21

updated test_ghosting

23f2c5e

I updated the test_ghosting script to work with the new ghosting function. Now the get_ghost_slice needs to be equal to the eligible area.

changed fun name from get_ghost_slice2 to get_ghost_slice

73c05c5

Update ghosting.py

43c64a5

tomaroberts requested changes Dec 20, 2021

View reviewed changes

Lucrezia-Cester added 6 commits December 21, 2021 08:32

removed the testing piece of code made redundant by the absolute value

f749f4b

updated indentation

c74b952

reverted back file because indentation caused an error

93dee58

Update test_ghosting.py

4ec2909

Removed constant outputting of image

c07d9fc

I fixed the problem where the script always outputted an image. Now it should only output if report_path == True

updated indentation

a078a39

tomaroberts linked an issue Dec 21, 2021 that may be closed by this pull request

Ghosting measurements on Philips Ingenia 1.5T #109

Closed

Lucrezia-Cester added 2 commits December 21, 2021 11:01

updated indentation

2fe7257

removed test made obsolete by asb value on ghosting formula

9f7510f

tomaroberts added this to the 0.5.2 milestone Dec 21, 2021

Lucrezia-Cester changed the base branch from release/0.5.2 to release/0.5.1 December 22, 2021 08:37

tomaroberts changed the title ~~updated ghosting script~~ Updated ghosting function – fixes sampling point issue Dec 22, 2021

tomaroberts changed the base branch from release/0.5.1 to release/0.5.2 December 22, 2021 10:28

tomaroberts merged commit 2c25632 into release/0.5.2 Dec 22, 2021

This was referenced Dec 22, 2021

Ghosting measurements on Philips Ingenia 1.5T #109

Closed

[HZN-99] Hazen produced ghosting values do not match ImageJ values #99

Closed

tomaroberts deleted the fix_ghosting_script branch February 16, 2022 09:26

This was referenced Feb 16, 2022

Ghosting script does not work for physicists #160

Closed

[HZN-51] Prevent ghosting from returning negative values #51

Closed

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Updated ghosting function – fixes sampling point issue #185

Updated ghosting function – fixes sampling point issue #185

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Updated ghosting function – fixes sampling point issue #185

Updated ghosting function – fixes sampling point issue #185

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