Mib 21: Add stitching script by mlnagy · Pull Request #131 · ionpath/mibilib

mlnagy · 2024-05-01T23:51:20Z

No description provided.

… i have access to project i'm testing

environment.yml

scripts/tiling/stitching.py

…rom channels

… file name; added margins

jaytarolli · 2024-07-03T22:52:56Z

scripts/stitching/stitching.py

+from mibidata import mibi_image as mi
 from mibidata import tiff
-import json
+from mibitracker.request_helpers import MibiRequests


Reordered the imports. Python style is to import 1) standard modules 2) modules installed with conda/pip 3) custom modules, such as those in the repo being worked on

jaytarolli · 2024-07-03T22:53:50Z

scripts/stitching/stitching.py

        if out_img is None:
-            out_img = np.zeros((h*shape_2d[0]+(h-1)*margin["y"], w*shape_2d[1]+(w-1)*margin["x"], ch_count), 
-                               dtype=fov_img.dtype)
+            out_img = np.zeros(


Here, and a bunch of other places, kept line lengths to <=80 characters

jaytarolli · 2024-07-03T22:54:21Z

scripts/stitching/stitching.py

+                    "fov" + "-" + str(
+                        f["runOrder"]).zfill(2) + "-" + fov_name) + ".tiff")
+
+        print(f'Stitching {run} - {roi}: {len(roi_fov_paths)} FOVs')


Made the print statement a bit more informative/readable

jaytarolli · 2024-07-03T22:54:56Z

scripts/stitching/stitching.py

+        f_split[0] = roi
+        out_mibi_tiff.set_fov_id(f_split[0], '/'.join(f_split))

+        if not out_folder:


Made out_folder an optional parameter, if omitted then it defaults to saving in the run_folder

See comment

jaytarolli · 2024-07-03T22:55:28Z

scripts/stitching/stitching.py

-                if coord["y"] < um_min_y:
-                    um_min_y = coord["y"]
-                roi_fov_paths.append(os.path.join(run_folder,"fov"+"-"+str(f["runOrder"]).zfill(2)+"-"+fov_name)+".tiff")
+    for r in run_json["rois"]:


I pulled out all the rest of the code from the with block

jaytarolli · 2024-07-03T22:55:48Z

scripts/stitching/stitching.py

                for t in range(MAX_TRIES):
                    try:
-                        run_id = mr.get('/runs/', params={'name': run}).json()['results'][0]['id']
+                        _ = mr.post('/images/', json=new_im_metadata)


No need for the ignored return value

jaytarolli · 2024-07-03T22:56:46Z

scripts/stitching/stitching.py

+            print(
+                f"Stitched MIBItiff, {out_path}, uploaded to MIBItracker.")
+
+def parse_args(args):


Instead of specifying variables in the script itself, let the users pass them as arguments when running it

jaytarolli · 2024-07-03T22:57:31Z

scripts/stitching/stitching.py

+    ''' Argument parsing helper function.   
+    '''
+    parser = argparse.ArgumentParser(
+        description='Script for creating a stitched ROI MIBItiff from a folder '


Moves the script description and argument help text to argparse so that it can be viewed with python stitching.py --help

jaytarolli · 2024-07-03T22:58:20Z

@mlnagy I made some changes and have added comments to my changes to give you context for why I did. I also tested it to some degree. Testing performed:

python .\stitching.py --run_folder "C:/Users/Jay Tarolli/data/M14/2024-05-30T21-45-35-7pass_largeROI": Success
python .\stitching.py --run_folder "C:/Users/Jay Tarolli/data/M14/2024-05-30T21-45-35-7pass_largeROI" --out_folder 'C:/Users/Jay Tarolli/data/M14/2024-05-30T21-45-35-7pass_largeROI_subset/subfolder': Success
python .\stitching.py --run_folder "C:/Users/Jay Tarolli/data/M14/2024-05-30T21-45-35-7pass_largeROI" --enforce_square: Sets enforce_square to True; canceled before TIFF generation
python .\stitching.py --run_folder "C:/Users/Jay Tarolli/data/M14/2024-05-30T21-45-35-7pass_largeROI" --upload_to_mibitracker: Sets upload_to_mibitracker to True, fails because URL, email, and password not specified
python .\stitching.py --run_folder "C:/Users/Jay Tarolli/data/M14/2024-05-30T21-45-35-7pass_largeROI" --upload_to_mibitracker --mibitracker_email [redacted] --mibitracker_password [redacted] --mibitracker_url [redacted]: MibiRequests instance created, verifying log in; canceled before upload
python .\stitching.py --run_folder "C:/Users/Jay Tarolli/data/M14/2024-05-30T21-45-35-7pass_largeROI": verified margin = {'x': 0, 'y': 0}
python .\stitching.py --run_folder "C:/Users/Jay Tarolli/data/M14/2024-05-30T21-45-35-7pass_largeROI" --fov_margin_size_x 10: verified margin = {'x': 10, 'y': 0}
python .\stitching.py --run_folder "C:/Users/Jay Tarolli/data/M14/2024-05-30T21-45-35-7pass_largeROI" --fov_margin_size_x 10 --fov_margin_size_y 2: verified margin = {'x': 10, 'y': 20}

therealjacinto · 2024-07-11T19:31:34Z

scripts/stitching/stitching.py

+
+MAX_TRIES = 5
+
+def combine_entity_by_name(roi_fov_paths, cols, rows, enforce_square, margin):


I see that we probably won't be needing enforce_square anymore now that mibitracker allows for non-square images. Do we want to at least change this so that it has the default value of False?

therealjacinto · 2024-07-11T19:33:28Z

scripts/stitching/stitching.py

+        int(max(w*shape_2d[1], h*shape_2d[0])), ref_metadata
+
+
+def stitch_fovs(run_folder, out_folder, session_dict, upload_to_mibitracker,


to make it clear that out_folder can be None, can we have it have the default value of None?

therealjacinto · 2024-07-11T19:33:46Z

scripts/stitching/stitching.py

+        f_split[0] = roi
+        out_mibi_tiff.set_fov_id(f_split[0], '/'.join(f_split))

+        if not out_folder:


See comment

therealjacinto · 2024-07-11T19:35:18Z

scripts/stitching/stitching.py

+from mibidata import tiff
+from mibitracker.request_helpers import MibiRequests
+
+MAX_TRIES = 5


Can we rename this and have a comment on what this is used for? Something like MAX_MIBITRACKER_REST_TRIES or something

therealjacinto · 2024-07-11T19:36:36Z

scripts/stitching/stitching.py

@@ -0,0 +1,325 @@
+""" Script for creating a stitched ROI MIBItiff from a folder of FOVs.


All methods in this file need a docstring explaining what the function does and what each argument is: https://peps.python.org/pep-0257/#multi-line-docstrings

jaytarolli · 2024-08-07T18:32:00Z

scripts/stitching/stitching.py

+
+import numpy as np
+
+sys.path.append('../..')


I think this is needed if a user is just using the mibilib conda env

mlnagy added 4 commits March 6, 2024 10:00

MIB-20 fix with replication due to astype conversion

49e9c1e

loosened pandas req

dfdaafe

MIB-21 script for stitching FOVs - init

8db0a94

fixes in script; all seems to work now; just need to test upload once…

02556e0

… i have access to project i'm testing

jaytarolli suggested changes May 3, 2024

View reviewed changes

mlnagy and others added 8 commits May 3, 2024 12:21

updated based on PR feedback: reverted pandas version; removed loop f…

8a61f0e

…rom channels

updated based on PR feedbacks

008cc0f

removed need to query mibitracker if not uploading; improved uploaded…

588b854

… file name; added margins

added nonsquare to stitch

9ad84fd

added use of set_image_size function

64d5bf8

fixes with nonsquare stitch

f1d1dc6

Add argparse for script parameters

015b35b

Verify args and small changes

13cfd06

jaytarolli reviewed Jul 3, 2024

View reviewed changes

Remove unused variable

9e4c179

therealjacinto requested changes Jul 11, 2024

View reviewed changes

Add README for the script

07d097e

jaytarolli reviewed Aug 7, 2024

View reviewed changes


		MAX_TRIES = 5

		def combine_entity_by_name(roi_fov_paths, cols, rows, enforce_square, margin):

		int(max(wshape_2d[1], hshape_2d[0])), ref_metadata


		def stitch_fovs(run_folder, out_folder, session_dict, upload_to_mibitracker,

		@@ -0,0 +1,325 @@
		""" Script for creating a stitched ROI MIBItiff from a folder of FOVs.

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mlnagy commented May 1, 2024

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jaytarolli commented Jul 3, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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jaytarolli commented Jul 3, 2024 •

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