v0.3.2 fixing erosion bug

Author: Corentin

.gitignore

@@ -171,4 +171,6 @@ debug_data/
 !binary_mask_sdh.tif
 data/*
 *intensity_plot.png
-*.idea
+*.idea
+cellpose.sh
+nohup.out

.python-version

@@ -1 +1 @@
-3.10.9
+3.10.11

myoquant/__main__.py

@@ -1,11 +1,27 @@
 import typer
 from rich.console import Console
+import pkg_resources
+
+__version__ = pkg_resources.get_distribution("myoquant").version
+__version_cellpose__ = pkg_resources.get_distribution("cellpose").version
+__version_stardist__ = pkg_resources.get_distribution("stardist").version
+__version_torch__ = pkg_resources.get_distribution("torch").version
+__version_tensorflow__ = pkg_resources.get_distribution("tensorflow").version
 
 from .commands.docs import app as docs_app
 from .commands import run_sdh, run_he, run_atp
 
 console = Console()
 
+
+def version_callback(value: bool):
+    if value:
+        print(
+            f"MyoQuant Version: {__version__} \nCellpose Version: {__version_cellpose__} \nStardist Version: {__version_stardist__} \nTorch Version: {__version_torch__} \nTensorflow Version: {__version_tensorflow__}"
+        )
+        raise typer.Exit()
+
+
 app = typer.Typer(
     name="MyoQuant",
     add_completion=False,
@@ -15,6 +31,17 @@
 app.add_typer(docs_app, name="docs", help="Generate documentation")
 
 
+@app.callback()
+def main(
+    version: bool = typer.Option(
+        None, "--version", callback=version_callback, is_eager=True
+    )
+):
+    """
+    MyoQuant Analysis Command Line Interface
+    """
+
+
 app.registered_commands += (
     run_sdh.app.registered_commands
     + run_he.app.registered_commands

myoquant/src/common_func.py

@@ -181,10 +181,10 @@ def extract_single_image(raw_image, df_props, index, erosion=None):
     surface_area = df_props.iloc[index, 1]
     cell_radius = math.sqrt(surface_area / math.pi)
     single_entity_mask = df_props.iloc[index, 9].copy()
-    erosion_size = cell_radius * (
-        erosion / 100
-    )  # Erosion in percentage of the cell radius
     if erosion is not None:
+        erosion_size = cell_radius * (
+            erosion / 100
+        )  # Erosion in percentage of the cell radius
         for i in range(int(erosion_size)):
             single_entity_mask = binary_erosion(
                 single_entity_mask, out=single_entity_mask

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "myoquant"
-version = "0.3.1"
+version = "0.3.2"
 description = "MyoQuant🔬: a tool to automatically quantify pathological features in muscle fiber histology images."
 authors = ["Corentin Meyer <[email protected]>"]
 maintainers = ["Corentin Meyer <[email protected]>"]