Merge pull request #647 from NEUBIAS/move-openij-python-to-module

Move OpenIJTIFF python to module/conda-package
NEUBIAS · Apr 24, 2024 · e2a8274 · e2a8274
2 parents 91f75b6 + f74abe7
commit e2a8274
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diff --git a/_includes/auto_threshold/auto_threshold_act1_skimage_napari.py b/_includes/auto_threshold/auto_threshold_act1_skimage_napari.py
@@ -1,10 +1,6 @@
 # %% [markdown]
 # ## Apply manual and automated thresholds
 
-# %%
-import sys
-sys.path.append("C:\\Users\\akhan\\python_course")
-
 # %%
 # initial imports
 import napari

diff --git a/_includes/auto_threshold/auto_threshold_act2_skimage_napari.py b/_includes/auto_threshold/auto_threshold_act2_skimage_napari.py
@@ -1,9 +1,6 @@
 # %% [markdown]
 # ## Apply automated thresholds in 3D
 
-# %%
-import sys
-sys.path.append("C:\\Users\\akhan\\python_course")
 
 # %%
 # initial imports

diff --git a/_includes/binarization/binarization_act1_skimage_napari.py b/_includes/binarization/binarization_act1_skimage_napari.py
@@ -1,10 +1,6 @@
 # %% [markdown]
 # ## Thresholding bright and dim cell
 
-# %%
-import sys
-sys.path.append("C:\\Users\\akhan\\python_course")
-
 # %%
 # Instantiate the napari viewer
 import napari

diff --git a/_includes/binarization/binarization_act2_skimage_napari.py b/_includes/binarization/binarization_act2_skimage_napari.py
@@ -1,10 +1,6 @@
 # %% [markdown]
 # ## Spots and threshold interval
 
-# %%
-import sys
-sys.path.append("C:\\Users\\akhan\\python_course")
-
 # %%
 # Instantiate the napari viewer
 import napari

diff --git a/_includes/connected_components/connected_components_act2_skimage_napari.py b/_includes/connected_components/connected_components_act2_skimage_napari.py
@@ -1,10 +1,6 @@
 # %% [markdown]
 # # 3D connected component labeling
 
-# %%
-import sys
-sys.path.append("C:\\Users\\akhan\\python_course")
-
 # %%
 # Import modules
 import napari

diff --git a/_includes/datatypes/datatypes_act1_skimage_napari.py b/_includes/datatypes/datatypes_act1_skimage_napari.py
@@ -1,10 +1,6 @@
 # %% [markdown]
 # ## Explore image data types and value ranges
 
-# %%
-import sys
-sys.path.append("C:\\Users\\akhan\\python_course")
-
 # %%
 # Import modules
 import napari

diff --git a/_includes/multidimensional_images/multidimensional_images_act1_skimage_napari.py b/_includes/multidimensional_images/multidimensional_images_act1_skimage_napari.py
@@ -1,11 +1,6 @@
 # %% [markdown]
 # ## Explore a 3D image
 
-# %%
-# Add folder with additional functions to the path
-import sys
-sys.path.append("/Users/tischer/Documents/training-resources/functions")
-
 # %%
 # Load the image
 from OpenIJTIFF import open_ij_tiff

diff --git a/_includes/multidimensional_images/multidimensional_images_act2_skimage_napari.py b/_includes/multidimensional_images/multidimensional_images_act2_skimage_napari.py
@@ -1,11 +1,6 @@
 # %% [markdown]
 # ## Explore a 3D multi-channel image
 
-# %%
-# Add folder with functions to path
-import sys
-sys.path.append("/Users/tischer/Documents/training-resources/functions")
-
 # %%
 # Load the image 
 from OpenIJTIFF import open_ij_tiff

diff --git a/_includes/multidimensional_images/multidimensional_images_act3_skimage_napari.py b/_includes/multidimensional_images/multidimensional_images_act3_skimage_napari.py
@@ -1,11 +1,6 @@
 # %% [markdown]
 # ## Inspect a 3D time-lapse image
 
-# %%
-# Add folder with functions to path
-import sys
-sys.path.append("/Users/tischer/Documents/training-resources/functions")
-
 # %%
 # Load the image
 from OpenIJTIFF import open_ij_tiff

diff --git a/_includes/multidimensional_images/multidimensional_images_act4_skimage_napari.py b/_includes/multidimensional_images/multidimensional_images_act4_skimage_napari.py
@@ -1,11 +1,6 @@
 # %% [markdown]
 # ## Explore a 5D image (3D image + channels + time)
 
-# %%
-# Add folder with functions to path
-import sys
-sys.path.append("/Users/tischer/Documents/training-resources/functions")
-
 # %%
 # Load the image
 from OpenIJTIFF import open_ij_tiff

diff --git a/_includes/projections/projections_act1_skimage_napari.py b/_includes/projections/projections_act1_skimage_napari.py
@@ -3,10 +3,6 @@
 #
 #
 
-# %%
-import sys
-sys.path.append("C:\\Users\\akhan\\python_course")
-
 # %%
 # Import python packages.
 from OpenIJTIFF import open_ij_tiff

diff --git a/_includes/spatial_calibration/spatial_calibration_act1_skimage_napari.py b/_includes/spatial_calibration/spatial_calibration_act1_skimage_napari.py
@@ -3,10 +3,6 @@
 # #### Requirements
 # - [skimage and napari](https://neubias.github.io/training-resources/tool_installation/index.html#skimage_napari)
 
-# %%
-import sys
-sys.path.append("/Users/tischer/Documents/training-resources/functions")
-
 # %%
 # Import python packages.
 from OpenIJTIFF import open_ij_tiff

diff --git a/_includes/spatial_calibration/spatial_calibration_act2_skimage_napari.py b/_includes/spatial_calibration/spatial_calibration_act2_skimage_napari.py
@@ -3,10 +3,6 @@
 # #### Requirements
 # - [skimage and napari](https://neubias.github.io/training-resources/tool_installation/index.html#skimage_napari)
 
-# %%
-import sys
-sys.path.append("/Users/tischer/Documents/training-resources/functions")
-
 # %%
 # Import python packages.
 from OpenIJTIFF import open_ij_tiff, save_ij_tiff

diff --git a/functions/OpenIJTIFF.py b/functions/OpenIJTIFF.py