Make this package a package

.github/workflows/python-build.yaml

@@ -0,0 +1,21 @@
+name: Build
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up python
+        uses: actions/setup-python@v4
+        with: 
+          python-version: ${{ matrix.python-version }}
+      - name: Install build dependencies
+        run: pip install --upgrade build
+      - name: Build package
+        run: python3 -m build
+      # TODO: add step to publish to pypi

README.md

@@ -1,2 +1,4 @@
+[![Build Python Package](https://github.com/lysogeny/ResolveTools/actions/workflows/python-build.yaml/badge.svg)](https://github.com/lysogeny/ResolveTools/actions/workflows/python-build.yaml)
+
 # resolve-tools
 Analyzing Resolve Data.

pyproject.toml

@@ -0,0 +1,42 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "resolve_tools"
+dependencies = [
+    # File formats
+    "readlif>=0.6.0",
+    "tifffile>=2022.5.4",
+    # Image processing
+    "scikit-image>=0.19.2",
+    "opencv-python>=4.7.0",
+    "mclahe@git+https://github.com/VincentStimper/mclahe",
+    # Missing dependency from mclahe
+    "tensorflow>=2.8.2",
+    # Various data analysis tools
+    "glmpca>=0.1.0",
+    "scikit-misc>=0.1.4",
+    "pandas>=1.4.2",
+    "numpy>=1.22.1",
+    "scipy>=1.8.1",
+    "openpyxl>=3.0.10",
+    "numba>=0.56.4",
+    "loompy>=3.0.7",
+    "scanpy>=1.9.1",
+]
+version = "0.0.1"
+authors = [
+  { name="Valentin Wüst", email="[email protected]" },
+]
+description = "Analyse Resolve Molecular Cartography data"
+readme = "README.md"
+requires-python = ">=3.7"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/anders-biostat/ResolveTools"
+"Bug Tracker" = "https://github.com/anders-biostat/ResolveTools/issues"

scripts/baysor/01.1_transcripts.py

@@ -1,8 +1,8 @@
 import sys
 sys.path.insert(0,'/data/')
 
-from ResolveTools.baysor.utils import counts_resolve_to_baysor
-from ResolveTools.utils.utils import printwtime
+from resolve_tools.baysor.utils import counts_resolve_to_baysor
+from resolve_tools.utils.utils import printwtime
 import re
 import os
 
@@ -14,4 +14,4 @@
 
 counts_resolve_to_baysor("/data/resolve/04_registration3D/"+filename,
                          "/data/baysor/02_transcripts_wmesmer/"+filename.replace(".txt","_baysor_wmesmer.txt"),
-                        segmaskpath="/data/confocal/02_mesmer_nuclei/Confocal_"+roikey+"_DAPI_mesmer_nuclei_post.npz")
+                        segmaskpath="/data/confocal/02_mesmer_nuclei/Confocal_"+roikey+"_DAPI_mesmer_nuclei_post.npz")

scripts/baysor/03.1_combine.py

@@ -1,7 +1,7 @@
 import os
 import sys
 sys.path.insert(0,'/data/')
-from ResolveTools.baysor.utils import combine_baysor_transcripts
+from resolve_tools.baysor.utils import combine_baysor_transcripts
 
 
 

scripts/baysor/scripts/final_01_process_simple.py

@@ -4,9 +4,9 @@
 import matplotlib.pyplot as plt
 from matplotlib.backends.backend_pdf import PdfPages
 
-from ResolveTools.baysor.utils import split_baysor_ROIs, assign_counts_from_Baysor
-from ResolveTools.baysor.visualization import plot_celltypedist
-from ResolveTools.utils.utils import printwtime
+from resolve_tools.baysor.utils import split_baysor_ROIs, assign_counts_from_Baysor
+from resolve_tools.baysor.visualization import plot_celltypedist
+from resolve_tools.utils.utils import printwtime
 
 ## Split Results
 

scripts/baysor/scripts/final_02_process_custom.py

@@ -4,9 +4,9 @@
 import matplotlib.pyplot as plt
 from matplotlib.backends.backend_pdf import PdfPages
 
-from ResolveTools.baysor.roi import apply_combine_baysor_output
-from ResolveTools.baysor.visualization import plot_celltypedist
-from ResolveTools.utils.utils import printwtime
+from resolve_tools.baysor.roi import apply_combine_baysor_output
+from resolve_tools.baysor.visualization import plot_celltypedist
+from resolve_tools.utils.utils import printwtime
 
 result = sys.argv[1] # results_N21_wmesmer_combined
 

scripts/baysor/scripts/final_03_add_region.py

@@ -2,8 +2,8 @@
 sys.path.insert(0,'/data/')
 import os
 
-from ResolveTools.utils.utils import printwtime
-from ResolveTools.segmentation.brainregions import add_region_toadata
+from resolve_tools.utils.utils import printwtime
+from resolve_tools.segmentation.brainregions import add_region_toadata
 
 result = sys.argv[1] # results_N21_wmesmer_combined
 

scripts/baysor/scripts/final_04_add_stain.py

@@ -2,8 +2,8 @@
 sys.path.insert(0,'/data/')
 import os
 
-from ResolveTools.utils.utils import printwtime
-from ResolveTools.baysor.utils import add_stain_to_ROI
+from resolve_tools.utils.utils import printwtime
+from resolve_tools.baysor.utils import add_stain_to_ROI
 
 result = sys.argv[1] # results_N21_wmesmer_combined
 

scripts/baysor/scripts/final_05_combine_final.py

@@ -2,8 +2,8 @@
 sys.path.insert(0,'/data/')
 import os
 
-from ResolveTools.utils.utils import printwtime
-from ResolveTools.baysor.utils import combine_adatas
+from resolve_tools.utils.utils import printwtime
+from resolve_tools.baysor.utils import combine_adatas
 
 result = sys.argv[1] # results_N21_wmesmer_combined
 

scripts/baysor/scripts/final_06_add_QC.py

@@ -6,10 +6,10 @@
 import numpy as np
 import pandas as pd
 import seaborn as sns
-from ResolveTools.utils.utils import printwtime
-from ResolveTools.analysis.post import read_add_combined
-from ResolveTools.segmentation.counts import read_loom
-from ResolveTools.analysis.pseudotime import get_human_glmpca_data, get_meanpseudotime, plot_PT_shares
+from resolve_tools.utils.utils import printwtime
+from resolve_tools.analysis.post import read_add_combined
+from resolve_tools.segmentation.counts import read_loom
+from resolve_tools.analysis.pseudotime import get_human_glmpca_data, get_meanpseudotime, plot_PT_shares
 
 result = sys.argv[1] # results_N21_wmesmer_combined
 resultfolder = "/data/baysor/04_baysor/"+result

scripts/baysor/scripts/final_07_assignment_plots.py

@@ -3,8 +3,8 @@
 import os
 import matplotlib.pyplot as plt
 
-from ResolveTools.baysor.visualization import plot_final_assignment_post
-from ResolveTools.utils.utils import printwtime
+from resolve_tools.baysor.visualization import plot_final_assignment_post
+from resolve_tools.utils.utils import printwtime
 
 ## Split Results
 

scripts/confocal/01.1_prepare.py

@@ -7,8 +7,8 @@
 import os
 import sys
 sys.path.insert(0,'/data/')
-from ResolveTools.image.utils import save_tiff
-from ResolveTools.image.lif import LifFile, read_lif_image
+from resolve_tools.image.utils import save_tiff
+from resolve_tools.image.lif import LifFile, read_lif_image
 
 from tqdm import tqdm
 
@@ -41,4 +41,4 @@ def make_small_max(name, factor=8):
 
 for name in tqdm(run1+run2):
     print(name)
-    make_small_max(name)
+    make_small_max(name)

scripts/confocal/01.2.1_clip_copy.py

@@ -9,12 +9,12 @@
 import sys
 sys.path.insert(0,'/data/')
 
-from ResolveTools.image.utils import save_tiff, claher, read_single_modality_confocal
-from ResolveTools.image.lif import LifFile, read_lif_image
-from ResolveTools.registration.registerSIFT import find_homography, warp_image, transform_coordinate, scale_homography,\
+from resolve_tools.image.utils import save_tiff, claher, read_single_modality_confocal
+from resolve_tools.image.lif import LifFile, read_lif_image
+from resolve_tools.registration.registerSIFT import find_homography, warp_image, transform_coordinate, scale_homography,\
                                                     get_transformed_corners
-from ResolveTools.segmentation.brainregions import processes_regionsegmentation_initial
-from ResolveTools.utils.utils import printwtime
+from resolve_tools.segmentation.brainregions import processes_regionsegmentation_initial
+from resolve_tools.utils.utils import printwtime
 
 def find_corners():
     printwtime("Loading Images")

scripts/confocal/01.4_make_max.py

@@ -3,8 +3,8 @@
 
 import sys
 sys.path.insert(0,'/data/')
-from ResolveTools.image.utils import save_tiff, save_tiff_from_float, claher, read_single_modality_confocal
-from ResolveTools.utils.utils import printwtime
+from resolve_tools.image.utils import save_tiff, save_tiff_from_float, claher, read_single_modality_confocal
+from resolve_tools.utils.utils import printwtime
 
 path = "/data/confocal/01_image/"
 images = os.listdir(path)
@@ -17,4 +17,4 @@
     img = read_single_modality_confocal(path+image, norm=False)
     save_tiff(path+image.replace(".tif","_max.tif"), img.max(axis=0)[None])
     save_tiff_from_float(path+image.replace(".tif","_max_claher.tif"), claher(img.max(axis=0))[None])
-    del img
+    del img

scripts/confocal/02.1_postprocess.py

@@ -9,8 +9,8 @@
 import sys
 sys.path.insert(0,'/data/')
 
-from ResolveTools.segmentation.postprocess import postprocess_raw_mesmer_masks
-from ResolveTools.utils.utils import printwtime
+from resolve_tools.segmentation.postprocess import postprocess_raw_mesmer_masks
+from resolve_tools.utils.utils import printwtime
 
 printwtime("Loading Mask")
 file = np.load("/data/confocal/"+sys.argv[1])

scripts/confocal/02.4_postprocess_meta.py

@@ -9,9 +9,9 @@
 import sys
 sys.path.insert(0,'/data/')
 
-from ResolveTools.segmentation.utils import segmentation_to_meta_df, save_sampled_boundary
+from resolve_tools.segmentation.utils import segmentation_to_meta_df, save_sampled_boundary
 from skimage.segmentation import find_boundaries
-from ResolveTools.utils.utils import printwtime
+from resolve_tools.utils.utils import printwtime
 import re
 
 filename = sys.argv[1]
@@ -25,4 +25,4 @@
 df.to_csv(filename.replace("post.npz", "post_meta.csv"))
 
 inner = find_boundaries(mask, mode="inner")
-save_sampled_boundary(mask, inner, filename.replace("post.npz", "post_boundary.npz"), N=60, seed=42)
+save_sampled_boundary(mask, inner, filename.replace("post.npz", "post_boundary.npz"), N=60, seed=42)

scripts/confocal/03.1_annotation_images.py

@@ -6,8 +6,8 @@
 
 import sys
 sys.path.insert(0,'/data/')
-from ResolveTools.image.utils import resize_shrink, read_single_modality_confocal
-from ResolveTools.utils.utils import printwtime
+from resolve_tools.image.utils import resize_shrink, read_single_modality_confocal
+from resolve_tools.utils.utils import printwtime
 
 factor = 2
 path = "/data/confocal/01_image/"
@@ -29,4 +29,4 @@
     final[..., 2] = dapimax
     final[..., 1] = wgamax
 
-    cv2.imwrite(pathout+'Confocal_'+roi+'_annotation_tempalte.jpg', (final*255).astype("H"), [cv2.IMWRITE_JPEG_QUALITY, 100])
+    cv2.imwrite(pathout+'Confocal_'+roi+'_annotation_tempalte.jpg', (final*255).astype("H"), [cv2.IMWRITE_JPEG_QUALITY, 100])

scripts/confocal/03.2_annotation_process.py

@@ -4,8 +4,8 @@
 
 import sys
 sys.path.insert(0,'/data/')
-from ResolveTools.segmentation.brainregions import processes_regionsegmentation_initial
-from ResolveTools.utils.utils import printwtime
+from resolve_tools.segmentation.brainregions import processes_regionsegmentation_initial
+from resolve_tools.utils.utils import printwtime
 
 path = "/data/confocal/03_annotation/"
 process = list(filter(lambda x: "_annotation.png" in x, os.listdir("/data/confocal/03_annotation")))
@@ -17,4 +17,4 @@
     referenceimg = "/data/confocal/01_image/Confocal_"+roi+"_DAPI.tif"
     annotpath = path+"Confocal_"+roi+"_annotated_regions.npz"
 
-    processes_regionsegmentation_initial(imagepath, referenceimg, annotpath)
+    processes_regionsegmentation_initial(imagepath, referenceimg, annotpath)

scripts/confocal/03.3_annotation_allmeta.py

@@ -6,8 +6,8 @@
 
 import sys
 sys.path.insert(0,'/data/')
-from ResolveTools.segmentation.brainregions import regionkey, regioncolors
-from ResolveTools.utils.utils import printwtime
+from resolve_tools.segmentation.brainregions import regionkey, regioncolors
+from resolve_tools.utils.utils import printwtime
 
 path = "/data/confocal/03_annotation/"
 files = list(filter(lambda x: "_annotated_regions.npz" in x, os.listdir("/data/confocal/03_annotation")))
@@ -23,4 +23,4 @@
 
 df = df.loc[[i for i in df.index if i in regionkey.keys()]].copy()
 df.index = [regionkey[i] for i in df.index]
-df.to_csv(path+"Confocal_annotation_overview.csv")
+df.to_csv(path+"Confocal_annotation_overview.csv")

scripts/resolve/03.1_register2D.py

@@ -9,12 +9,12 @@
 import sys
 sys.path.insert(0,'/data/')
 
-from ResolveTools.image.utils import save_tiff, claher, resize_shrink
-from ResolveTools.registration.registerSIFT import find_homography, find_homographies, warp_image,\
+from resolve_tools.image.utils import save_tiff, claher, resize_shrink
+from resolve_tools.registration.registerSIFT import find_homography, find_homographies, warp_image,\
                                                     transform_coordinate, scale_homography, get_transformed_corners,\
                                                     homography_shift_target
-from ResolveTools.registration.registerTiles import tile_2Dimage
-from ResolveTools.utils.utils import printwtime
+from resolve_tools.registration.registerTiles import tile_2Dimage
+from resolve_tools.utils.utils import printwtime
 
 name = sys.argv[1]
 

scripts/resolve/04.1_register3D.py

@@ -1,7 +1,7 @@
 import sys
 sys.path.insert(0,'/data/')
-from ResolveTools.registration.register3D import register_3d_counts
-from ResolveTools.utils.utils import printwtime
+from resolve_tools.registration.register3D import register_3d_counts
+from resolve_tools.utils.utils import printwtime
 
 import re
 import os
@@ -22,4 +22,4 @@
                        "/data/resolve/04_registration3D/T6GBM_"+name+"_transcripts_registered3D.txt",
                        segmentationfile="/data/confocal/02_mesmer_nuclei/Confocal_" + name + "_DAPI_mesmer_nuclei_post.npz", segmentationkey="mask_post",
                        verbose=True, binsize=1000, shiftstep=0.4,
-                       plotfile="/data/resolve/02_QC/T6GBM_" + name + "_zShift.jpeg", plottitle=name)
+                       plotfile="/data/resolve/02_QC/T6GBM_" + name + "_zShift.jpeg", plottitle=name)

scripts/resolve/05.1_counts_naive.py

@@ -2,8 +2,8 @@
 import re
 import sys
 sys.path.insert(0,'/data/')
-from ResolveTools.segmentation.counts import assign_counts_from_segmentation
-from ResolveTools.utils.utils import printwtime
+from resolve_tools.segmentation.counts import assign_counts_from_segmentation
+from resolve_tools.utils.utils import printwtime
 
 path = "/data/resolve/04_registration3D/"
 
@@ -18,4 +18,4 @@
                                     "/data/confocal/02_mesmer_nuclei/Confocal_" + name + "_DAPI_mesmer_nuclei_post_meta.csv",
                                     "/data/resolve/05_counts_naive/T6GBM_" + name + "_counts_naive.loom",
                                     name,
-                                    True)
+                                    True)