Systematic Approach of adding notebooks

.gitignore

@@ -11,3 +11,4 @@ build
 .*.swp
 .mha
 .jpg
+docs/source/hello.ipynb

docs/source/conf.py

@@ -14,6 +14,79 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 
+# PreProcessing:
+
+from pathlib import Path
+import shutil
+
+
+# Copy notebooks to source
+
+print("########################")
+print("########################")
+print("########################")
+print("########################")
+
+ROOT_DIR = Path.cwd().parent.parent
+print(ROOT_DIR )
+COPYFROM = ROOT_DIR 
+COPYTO = ROOT_DIR / "docs" / "source"
+print(COPYFROM)
+print(COPYTO)
+folders = ["Python", "Data", "Utilities"]
+for num, folder in enumerate(folders): 
+    print("######")
+    folder_from = COPYFROM/ folder
+    folder_to = COPYTO /folder
+    print(f"{folder_from}")
+    print(f"{folder_to}")
+    shutil.copytree(folder_from, folder_to)
+    print("******DONE*******")
+
+# delete all notebooks that are not wanted
+NEWLOCATION = ROOT_DIR / "docs" / "source"
+exclude_notobooks = [
+"Python/00_Setup.ipynb",
+#"Python/01_Image_Basics.ipynb",
+#"Python/02_Pythonic_Image.ipynb",
+#"Python/03_Image_Details.ipynb",
+#"Python/04_Image_Display.ipynb",
+#"Python/05_Results_Visualization.ipynb",
+#"Python/10_matplotlibs_imshow.ipynb",
+"Python/11_Progress.ipynb",
+#"Python/20_Expand_With_Interpolators.ipynb",
+#"Python/21_Transforms_and_Resampling.ipynb",
+#"Python/22_Transforms.ipynb",
+#"Python/300_Segmentation_Overview.ipynb",
+#"Python/30_Segmentation_Region_Growing.ipynb",
+#"Python/31_Levelset_Segmentation.ipynb",
+#"Python/32_Watersheds_Segmentation.ipynb",
+#"Python/33_Segmentation_Thresholding_Edge_Detection.ipynb",
+#"Python/34_Segmentation_Evaluation.ipynb",
+#"Python/35_Segmentation_Shape_Analysis.ipynb",
+#"Python/36_Microscopy_Colocalization_Distance_Analysis.ipynb",
+#"Python/51_VH_Segmentation1.ipynb",
+"Python/55_VH_Resample.ipynb",
+#"Python/56_VH_Registration1.ipynb",
+#"Python/60_Registration_Introduction.ipynb",
+#"Python/61_Registration_Introduction_Continued.ipynb",
+#"Python/62_Registration_Tuning.ipynb",
+#"Python/63_Registration_Initialization.ipynb",
+"Python/64_Registration_Memory_Time_Tradeoff.ipynb",
+"Python/65_Registration_FFD.ipynb",
+"Python/66_Registration_Demons.ipynb",
+#"Python/67_Registration_Semiautomatic_Homework.ipynb",
+#"Python/68_Registration_Errors.ipynb",
+#"Python/69_x-ray-panorama.ipynb",
+#"Python/70_Data_Augmentation.ipynb",
+#"Python/71_Trust_But_Verify.ipynb",
+]
+
+for nb in exclude_notobooks:
+    excluded_notebook = NEWLOCATION/nb
+    print(excluded_notebook)
+    excluded_notebook.unlink()
+
 
 # -- Project information -----------------------------------------------------
 
@@ -33,8 +106,9 @@
     'sphinx_copybutton',
     'nbsphinx'
 ]
+nbsphinx_timeout = 10000 
 nbsphinx_allow_errors = True
-nbsphinx_execute = 'never'
+#nbsphinx_execute = 'never'
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -55,4 +129,4 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+#html_static_path = ['_static']

docs/source/index.rst

@@ -9,9 +9,46 @@ Contents can be used for:
 * As a basis for your teaching activities.  
 * As a basis for your research activities.  
 
-
-
-
+.. toctree::
+    :maxdepth: 2
+    :glob:
+
+    Python/00_Setup.ipynb
+    Python/01_Image_Basics.ipynb
+    Python/02_Pythonic_Image.ipynb
+    Python/03_Image_Details.ipynb
+    Python/04_Image_Display.ipynb
+    Python/05_Results_Visualization.ipynb
+    Python/10_matplotlibs_imshow.ipynb
+    Python/11_Progress.ipynb
+    Python/20_Expand_With_Interpolators.ipynb
+    Python/21_Transforms_and_Resampling.ipynb
+    Python/22_Transforms.ipynb
+    Python/300_Segmentation_Overview.ipynb
+    Python/30_Segmentation_Region_Growing.ipynb
+    Python/31_Levelset_Segmentation.ipynb
+    Python/32_Watersheds_Segmentation.ipynb
+    Python/33_Segmentation_Thresholding_Edge_Detection.ipynb
+    Python/34_Segmentation_Evaluation.ipynb
+    Python/35_Segmentation_Shape_Analysis.ipynb
+    Python/36_Microscopy_Colocalization_Distance_Analysis.ipynb
+    Python/51_VH_Segmentation1.ipynb
+    Python/55_VH_Resample.ipynb
+    Python/56_VH_Registration1.ipynb
+    Python/60_Registration_Introduction.ipynb
+    Python/61_Registration_Introduction_Continued.ipynb
+    Python/62_Registration_Tuning.ipynb
+    Python/63_Registration_Initialization.ipynb
+    Python/64_Registration_Memory_Time_Tradeoff.ipynb
+    Python/65_Registration_FFD.ipynb
+    Python/66_Registration_Demons.ipynb
+    Python/67_Registration_Semiautomatic_Homework.ipynb
+    Python/68_Registration_Errors.ipynb
+    Python/69_x-ray-panorama.ipynb
+    Python/70_Data_Augmentation.ipynb
+    Python/71_Trust_But_Verify.ipynb
+
+
 
 Repository on GitHub:
 https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks