Raw input preview #356

paskino · 2023-07-17T09:56:09Z

Should close #383

This PR did not pass the tests. Part of the work has been used in a new PR #410.

Adds preview button to the raw input dialog.
hides slider in the preview dialog (see hide option for slider #384)
hides one of the axes in 2D viewer preview (merged hide axis when creating viewer 2D #408)
Tested on knee data and not working. A working version has been found in another branch after removing the fortran ordering. (@paskino)
add unit tests (or not?)
run unit tests. At the moment many are failing (@paskino)

Not to be done in this PR:

test the code for dimensionality = 2. Opened Add tests for raw input of dimension 2 #404
test on web viewer, opened Web viewers errors #400
Remove fortran ordering from the raw input dialog (see Remove fortran order #390)

Wrappers/Python/ccpi/viewer/ui/dialogs.py

… formats

Wrappers/Python/ccpi/viewer/ui/dialogs.py

lauramurgatroyd

This worked great with the 16bit dataset that I tried, but I had problems with an 8bit dataset...
The preview cut the slice in half:

But when pressing 'OK' with those same settings, it loaded fine:

Wrappers/Python/ccpi/viewer/ui/dialogs.py

lauramurgatroyd · 2023-07-31T09:31:06Z

Wrappers/Python/ccpi/viewer/ui/dialogs.py

+        if dimensionality == 3:
+            # read the centre slice
+            slice_size = shape[1]*shape[0]
+            offset = shape[2]*slice_size//2
+
+        rawfname = os.path.join(tempfile.gettempdir(),"test.raw")
+
+        offset = offset * bytes_per_element
+        slices_to_read = 1
+        if shape[2] > 1:
+            slices_to_read = 2
+        with open(self.fname, 'br') as f:
+            f.seek(offset)
+            raw_data = f.read(slice_size*bytes_per_element* slices_to_read)
+            with open(rawfname, 'wb') as f2:
+                f2.write(raw_data)
+
+        reader2 = vtk.vtkImageReader2()
+        reader2.SetFileName(rawfname)
+
+        vtktype = Converter.dtype_name_to_vtkType[dt.name]
+        reader2.SetDataScalarType(vtktype)
+
+        if isBigEndian:
+            reader2.SetDataByteOrderToBigEndian()
+        else:
+            reader2.SetDataByteOrderToLittleEndian()
+
+        reader2.SetFileDimensionality(len(shape))
+        vtkshape = shape[:]
+        if not isFortran:
+            # need to reverse the shape (again)
+            vtkshape = shape[::-1]


I would suggest using the RawCroppedReader here instead, to avoid repetition of code

I used the cilRawCroppedReader but it gave the wrong output, which means that selecting from the dialog Fortran or C-order would preview a correct but different slice. In this case the preview would not be useful and the user might select open with the wrong setting.

This did not happen with the above code.

I updated cilRawCroppedReader with the code above. I haven't done more testing of this except using cilviewer to load a raw file.

@paskino is this conversation resolved or should we do more tests?

Co-authored-by: Laura Murgatroyd <[email protected]>

paskino · 2023-09-14T17:02:45Z

This worked great with the 16bit dataset that I tried, but I had problems with an 8bit dataset... The preview cut the slice in half:

But when pressing 'OK' with those same settings, it loaded fine:

Could you share the dataset?

… raw_input_preview

Wrappers/Python/ccpi/viewer/ui/dialogs.py

DanicaSTFC · 2024-04-10T17:46:25Z

Wrappers/Python/ccpi/viewer/ui/dialogs.py

+                central_slice = 'z'
+            else:
+                shape = (dimZ, dimY, dimX)
+                central_slice = 'x'


I added
if dimensionality == 3: if isFortran: shape = (dimX, dimY, dimZ) central_slice = 'z' else: shape = (dimZ, dimY, dimX) central_slice = 'x'

This means that the axes in the preview are wrong. We need to rotate them.

I did not test the code for dimensionality = 2, I need data for it.

This is now added to the preview.

Notice that we should also swap the axis labels when loading the whole image. This would be done in the application that uses the viewer, not in this dialog.

… raw_input_preview

remove commented out code

DanicaSTFC · 2024-04-30T13:50:11Z

This worked great with the 16bit dataset that I tried, but I had problems with an 8bit dataset... The preview cut the slice in half:
But when pressing 'OK' with those same settings, it loaded fine:

Could you share the dataset?

Data has been shared in Tomography-Data, DVC

The "file 40891_8bit_1431-1260-1335" is not uploaded correctly with the settings indicated by @lauramurgatroyd

By editing the fortran ordering the image is uploaded correctly, this work is currently stored in another branch

Wrappers/Python/ccpi/viewer/ui/dialogs.py

paskino · 2024-05-15T13:59:44Z

Probably we should rename Size XYZ to height width and number of images as done in ImageJ
This would render the Fortran thing useless.

DanicaSTFC · 2024-05-15T14:36:51Z

Probably we should rename Size XYZ to height width and number of images as done in ImageJ This would render the Fortran thing useless.

If we do so we should add an option in the app where the user can rename the labels eg. when saving images for research papers and investigating their system

paskino · 2024-05-15T21:47:13Z

If we do so we should add an option in the app where the user can rename the labels eg. when saving images for research papers and investigating their system

Yes, but that would be and advanced feature. So far I'd be happy if the dialog required the appropriate information and used it well. The axis labels defaults could, on first instance, remain X,Y and Z.

paskino · 2024-05-15T21:51:02Z

The probable culprit of the failing unit tests is the change in the conversion.py

DanicaSTFC · 2024-05-17T14:05:13Z

If we do so we should add an option in the app where the user can rename the labels eg. when saving images for research papers and investigating their system

Yes, but that would be and advanced feature. So far I'd be happy if the dialog required the appropriate information and used it well. The axis labels defaults could, on first instance, remain X,Y and Z.

I opened a new issue for this #406. The topic should be addressed in #390 as we will not address this here. I opened a new issue #407 for the advanced feature

DanicaSTFC · 2024-05-31T14:25:37Z

Closed as superseded by #410

paskino added 8 commits June 17, 2023 22:25

adding output as matplotlib canvas

c765603

working preview dialog

fe5d720

working test

be5cb4e

set vtk reader scalar type

9c334e7

working dialog no matplotlib

555f7f4

working dialog without matplotlib

19e6fd5

removed commented out code

5f758fc

delete temp file on dialog close

bd775b3

paskino commented Jul 27, 2023

View reviewed changes

Wrappers/Python/ccpi/viewer/ui/dialogs.py Outdated Show resolved Hide resolved

paskino added 2 commits July 28, 2023 16:17

simplifies code. Add multislice preview. Allows user to set supported…

ce5f180

… formats

removed test file

f7342ef

paskino marked this pull request as ready for review July 29, 2023 02:33

paskino commented Jul 29, 2023

View reviewed changes

Wrappers/Python/ccpi/viewer/ui/dialogs.py Outdated Show resolved Hide resolved

remove print, add logging

99c2c50

paskino changed the base branch from raw_input_preview to master July 31, 2023 08:17

paskino added 2 commits July 31, 2023 09:21

added to docstring

5302f23

added to CHANGELOG

ab73037

lauramurgatroyd requested changes Jul 31, 2023

View reviewed changes

lauramurgatroyd reviewed Jul 31, 2023

View reviewed changes

Apply suggestions from code review

cbe150c

Co-authored-by: Laura Murgatroyd <[email protected]>

paskino added 6 commits September 15, 2023 09:42

Merge branch 'master' into raw_input_preview

148276f

use cilRawCroppedReader

ce4eca4

use cilRawCroppedReader

c297efc

Merge branch 'raw_input_preview' of github.com:paskino/CILViewer into…

b7ae42f

… raw_input_preview

save state of dialog

320604b

save the dialog and reapply state

0ad670c

paskino assigned casperdcl and paskino Nov 2, 2023

save the dialog and reapply state

fac0127

casperdcl reviewed Mar 28, 2024

View reviewed changes

Wrappers/Python/ccpi/viewer/ui/dialogs.py Outdated Show resolved Hide resolved

DanicaSTFC added 5 commits April 10, 2024 17:01

Remove snooper and add edits on dtype by Casper

bdcfb31

Make supported typesconsistent

3f40f61

Add title preview

6918c82

Remove help icon from the dialogs

7a8b286

Add maximize flag to preview

38801bd

DanicaSTFC requested changes Apr 10, 2024

View reviewed changes

paskino added 2 commits April 15, 2024 23:44

Merge branch 'raw_input_preview' of github.com:paskino/CILViewer into…

cc854ba

… raw_input_preview

update cilBaseCroppedReader as it failed

c210597

remove commented out code

paskino force-pushed the raw_input_preview branch from 7418344 to c210597 Compare April 15, 2024 23:07

DanicaSTFC linked an issue Apr 25, 2024 that may be closed by this pull request

Raw input preview #383

Closed

DanicaSTFC mentioned this pull request Apr 30, 2024

hide option for slider #384

Closed

DanicaSTFC requested changes May 1, 2024

View reviewed changes

Wrappers/Python/ccpi/viewer/ui/dialogs.py Outdated Show resolved Hide resolved

DanicaSTFC added this to the Version 24.0.0 milestone May 2, 2024

DanicaSTFC added 3 commits May 16, 2024 14:21

pull branch

37eb987

Merge edits properly

799a4b6

set slider to false in the dialog

6dabed0

DanicaSTFC added 3 commits May 17, 2024 15:29

Merge master

c0d872e

Hide label axis in preview

f60d302

Delete duplicate line

f089d5a

paskino mentioned this pull request May 24, 2024

New Dialog for raw input preview #410

Merged

8 tasks

DanicaSTFC mentioned this pull request May 30, 2024

Improvements to raw input dialogue TomographicImaging/iDVC#26

Open

3 tasks

DanicaSTFC closed this May 31, 2024

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Raw input preview #356

Raw input preview #356

paskino commented Jul 17, 2023 •

edited by DanicaSTFC

Loading

lauramurgatroyd left a comment

lauramurgatroyd Jul 31, 2023

paskino Apr 15, 2024 •

edited

Loading

DanicaSTFC Apr 30, 2024

paskino commented Sep 14, 2023

DanicaSTFC Apr 10, 2024

DanicaSTFC Apr 11, 2024

paskino Apr 15, 2024

paskino Apr 15, 2024

DanicaSTFC commented Apr 30, 2024 •

edited

Loading

paskino commented May 15, 2024 •

edited

Loading

DanicaSTFC commented May 15, 2024

paskino commented May 15, 2024

paskino commented May 15, 2024

DanicaSTFC commented May 17, 2024 •

edited

Loading

DanicaSTFC commented May 31, 2024

Raw input preview #356

Raw input preview #356

Conversation

paskino commented Jul 17, 2023 • edited by DanicaSTFC Loading

lauramurgatroyd left a comment

Choose a reason for hiding this comment

lauramurgatroyd Jul 31, 2023

Choose a reason for hiding this comment

paskino Apr 15, 2024 • edited Loading

Choose a reason for hiding this comment

DanicaSTFC Apr 30, 2024

Choose a reason for hiding this comment

paskino commented Sep 14, 2023

DanicaSTFC Apr 10, 2024

Choose a reason for hiding this comment

DanicaSTFC Apr 11, 2024

Choose a reason for hiding this comment

paskino Apr 15, 2024

Choose a reason for hiding this comment

paskino Apr 15, 2024

Choose a reason for hiding this comment

DanicaSTFC commented Apr 30, 2024 • edited Loading

paskino commented May 15, 2024 • edited Loading

DanicaSTFC commented May 15, 2024

paskino commented May 15, 2024

paskino commented May 15, 2024

DanicaSTFC commented May 17, 2024 • edited Loading

DanicaSTFC commented May 31, 2024

paskino commented Jul 17, 2023 •

edited by DanicaSTFC

Loading

paskino Apr 15, 2024 •

edited

Loading

DanicaSTFC commented Apr 30, 2024 •

edited

Loading

paskino commented May 15, 2024 •

edited

Loading

DanicaSTFC commented May 17, 2024 •

edited

Loading