- Fix: broken assertion (#110).

- Fix: ome2histocat stripps .tiff file ending from masks (#111).

.github/workflows/docs.yml

@@ -23,7 +23,7 @@ jobs:
         with:
           docs-folder: docs/
           build-command: make html
-          pre-build-command: python -m pip install --upgrade pip && pip install poetry==1.1.5 && poetry config virtualenvs.create false && poetry install
+          pre-build-command: python -m pip install --upgrade pip && pip install poetry==1.1.6 && poetry config virtualenvs.create false && poetry install
       - name: Commit documentation changes
         run: |
           cp -r docs/build/html/* gh-pages/

.github/workflows/test_and_deploy.yml

@@ -31,7 +31,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install poetry==1.1.5
+          pip install poetry==1.1.6
           poetry install
         env:
           POETRY_VIRTUALENVS_CREATE: false
@@ -55,7 +55,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install poetry==1.1.5
+          pip install poetry==1.1.6
           poetry install --no-dev
         env:
           POETRY_VIRTUALENVS_CREATE: false

CHANGELOG.md

@@ -5,6 +5,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [2.1.7] - 2021-05-21
+- Fix: broken assertion (#110).
+- Fix: ome2histocat stripps .tiff file ending from masks (#111).
+
 ## [2.1.6] - 2021-03-16
 - Allows `mcdfolder_to_imcfolder` to convert data from sub-folders in zip file.
 

docs/source/quickstart.md

@@ -29,7 +29,7 @@ Version 1.x documentation (deprecated): https://imctools.readthedocs.io
 
 Preferable way to install `imctools` is via official PyPI registry. Please define package version explicitly in order to avoid incompatibilities between v1.x and v2.x versions:
 ```
-pip install imctools==2.1.4
+pip install imctools==2.1.7
 ```
 In old IMC segmentation pipelines versions 1.x should be used!
 ```

imctools/__init__.py

@@ -6,4 +6,4 @@
 
 __author__ = """Vito Zanotelli, Anton Rau"""
 __email__ = "[email protected], [email protected]"
-__version__ = "2.1.6"
+__version__ = "2.1.7"

imctools/converters/mcdfolder2imcfolder.py

@@ -75,10 +75,10 @@ def mcdfolder_to_imcfolder(
     tic = timeit.default_timer()
 
     mcdfolder_to_imcfolder(
-        # Path("/home/anton/Downloads/20170905_Fluidigmworkshopfinal_SEAJa.zip"),
+        Path("/home/anton/Data/ImcSegmentationPipelineV2/20191202_HuBMAP_LympNode_ED.zip"),
         # "/home/anton/Downloads/20170905_Fluidigmworkshopfinal_SEAJa",
         # "/home/anton/Data/forAnton_MCD/6505_Lympho",
-        "/home/anton/Downloads/IMMUcan_Batch20201113_10042702-GU-VAR-TIS-01-IMC-01.zip",
+        # "/home/anton/Downloads/IMMUcan_Batch20201113_10042702-GU-VAR-TIS-01-IMC-01.zip",
         # "/home/anton/Documents/merrick/IMC/20200904_MS_XRF_epithelial_panel_4_titration.zip",
         # "/home/anton/Documents/IMC Workshop 2019/Data/iMC_workshop_2019/20190919_FluidigmBrCa_SE",
         # "/home/anton/Downloads/test",

imctools/converters/ome2analysis.py

@@ -34,13 +34,13 @@ def get_metals_from_panel(
 
     if panel_csv_file is not None:
 
-        pannel = pd.read_csv(panel_csv_file)
-        if pannel.shape[1] > 1:
-            selected = pannel[usedcolumn]
-            assert selected.any() == 0 or selected.any() == 1, f"Values in 'usedcolumn' column should contain only 0/1"
-            metals = [str(n) for s, n in zip(selected, pannel[metalcolumn]) if s]
+        panel = pd.read_csv(panel_csv_file)
+        if panel.shape[1] > 1:
+            selected = panel[usedcolumn]
+            assert selected.isin((0, 1)).all(), f"Values in 'usedcolumn' column should contain only 0/1"
+            metals = panel.loc[selected == 1, metalcolumn].tolist()
         else:
-            metals = [pannel.columns[0]] + pannel.iloc[:, 0].tolist()
+            metals = [panel.columns[0]] + panel.iloc[:, 0].tolist()
 
     if sort_channels:
         if metals is not None:
@@ -187,9 +187,9 @@ def omefolder_to_analysisfolder(
     # )
 
     omefolder_to_analysisfolder(
-        "/home/anton/Downloads/imc_folder",
+        "/home/anton/Downloads/imc_folder_v2",
         "/home/anton/Downloads/analysis_folder",
-        "/home/anton/Downloads/example_panel.csv",
+        "/home/anton/Data/ImcSegmentationPipelineV2/hubmap_processed_v2/panel.csv",
         [("ilastik", "_ilastik", True), ("full", "_full", False)],
         metalcolumn="Metal Tag",
     )

imctools/converters/ome2histocat.py

@@ -68,9 +68,7 @@ def omefile_to_histocatfolder(
     if mask_file is not None:
         if isinstance(mask_file, str):
             mask_file = Path(mask_file)
-        fn_mask_base = mask_file.stem
-        fn_mask_new = output_folder / fn_mask_base
-        shutil.copy2(mask_file, fn_mask_new)
+        shutil.copy2(mask_file, output_folder)
 
 
 def omefolder_to_histocatfolder(
@@ -127,8 +125,9 @@ def omefolder_to_histocatfolder(
     tic = timeit.default_timer()
 
     omefolder_to_histocatfolder(
-        Path("/home/anton/Downloads/imc_folder/20170905_Fluidigmworkshopfinal_SEAJa"),
+        Path("/home/anton/Downloads/imc_folder_v2/20191203_HuBMAP_LN"),
         Path("/home/anton/Downloads/tiff_folder"),
+        mask_folder="/home/anton/Data/ImcSegmentationPipelineV2/hubmap_processed_v2/masks",
     )
 
     print(timeit.default_timer() - tic)