From 35a8286f768b18b9bba33ce6c8aa093ef6a6f816 Mon Sep 17 00:00:00 2001
From: kolibril13 <44469195+kolibril13@users.noreply.github.com>
Date: Wed, 10 Nov 2021 12:06:52 +0100
Subject: [PATCH 01/21] autocopy

---
 docs/source/conf.py   | 24 ++++++++++++++++++++++++
 docs/source/index.rst | 39 ++++++++++++++++++++++++++++++++++++++-
 2 files changed, 62 insertions(+), 1 deletion(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index aabed235..a7f78c4a 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -14,6 +14,30 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 
+# PreProcessing:
+from pathlib import Path
+import shutil
+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*******")
 
 # -- Project information -----------------------------------------------------
 
diff --git a/docs/source/index.rst b/docs/source/index.rst
index ef93a29f..6de7bd33 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -9,7 +9,44 @@ 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
 
 
 

From 40b85653ddf454ae86ad14dcf0167d572b3d27ba Mon Sep 17 00:00:00 2001
From: kolibril13 <44469195+kolibril13@users.noreply.github.com>
Date: Wed, 10 Nov 2021 12:44:43 +0100
Subject: [PATCH 02/21] added  delete script

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index aa3aedb4..eb47f27a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,3 +11,4 @@ build
 .*.swp
 .mha
 .jpg
+docs/source/hello.ipynb # local helper script 

From 1f97ca4b7eb0b027978203ee64903cfbc12ab126 Mon Sep 17 00:00:00 2001
From: kolibril13 <44469195+kolibril13@users.noreply.github.com>
Date: Wed, 10 Nov 2021 12:45:26 +0100
Subject: [PATCH 03/21] new delete script

---
 docs/source/conf.py              |  2 +-
 docs/source/delete_temp_files.py | 11 ++++++
 docs/source/hello.ipynb          | 64 ++++++++++++++++++++++++++++++++
 3 files changed, 76 insertions(+), 1 deletion(-)
 create mode 100644 docs/source/delete_temp_files.py
 create mode 100644 docs/source/hello.ipynb

diff --git a/docs/source/conf.py b/docs/source/conf.py
index a7f78c4a..f6c71fc7 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -79,4 +79,4 @@
 # 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']
\ No newline at end of file
+#html_static_path = ['_static']
diff --git a/docs/source/delete_temp_files.py b/docs/source/delete_temp_files.py
new file mode 100644
index 00000000..440add46
--- /dev/null
+++ b/docs/source/delete_temp_files.py
@@ -0,0 +1,11 @@
+import shutil
+from pathlib import Path
+
+DOCS_SOURCE_DIR = Path.cwd()  / "source"
+print(DOCS_SOURCE_DIR)
+
+folders = ["Python", "Data", "Utilities"]
+for folder in folders:
+    print(DOCS_SOURCE_DIR / folder)
+    shutil.rmtree(DOCS_SOURCE_DIR/folder)
+
diff --git a/docs/source/hello.ipynb b/docs/source/hello.ipynb
new file mode 100644
index 00000000..b935cc9b
--- /dev/null
+++ b/docs/source/hello.ipynb
@@ -0,0 +1,64 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/Users/jan-hendrik/projects/SimpleITK-Notebooks\n"
+     ]
+    }
+   ],
+   "source": [
+    "from pathlib import Path\n",
+    "import shutil\n",
+    "\n",
+    "ROOT_DIR = Path.cwd().parent.parent\n",
+    "print(ROOT_DIR )\n",
+    "\n",
+    "COPYFROM = ROOT_DIR \n",
+    "COPYTO = ROOT_DIR / \"docs\" / \"source\"\n",
+    "print(COPYFROM)\n",
+    "print(COPYTO)\n",
+    "folders = [\"Python\", \"Data\", \"Utilities\"]\n",
+    "for num, folder in enumerate(folders): \n",
+    "    print(\"######\")\n",
+    "    folder_from = COPYFROM/ folder\n",
+    "    folder_to = COPYTO /folder\n",
+    "    print(f\"{folder_from}\")\n",
+    "    print(f\"{folder_to}\")\n",
+    "    shutil.copytree(folder_from, folder_to)\n",
+    "    print(\"******DONE*******\")\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "interpreter": {
+   "hash": "7ebf924f33491c921954fca832147f8f5cb2261a32d05c905747d88e8d31766a"
+  },
+  "kernelspec": {
+   "display_name": "Python 3.8.12 64-bit ('sitk': conda)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.12"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

From 365af5779d3abffbc709ffa9b5b5ed5f9fbcbe73 Mon Sep 17 00:00:00 2001
From: kolibril13 <44469195+kolibril13@users.noreply.github.com>
Date: Wed, 10 Nov 2021 12:57:04 +0100
Subject: [PATCH 04/21] delete non needed notebooks

---
 docs/source/conf.py | 47 ++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 46 insertions(+), 1 deletion(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index f6c71fc7..eff47205 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -24,7 +24,7 @@
 
 ROOT_DIR = Path.cwd().parent.parent
 print(ROOT_DIR )
-
+# Copy notebooks to source
 COPYFROM = ROOT_DIR 
 COPYTO = ROOT_DIR / "docs" / "source"
 print(COPYFROM)
@@ -39,6 +39,51 @@
     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 -----------------------------------------------------
 
 project = 'SimpleITK-Notebooks'

From ffcfb7178ccba043e151a69d69c4cd9af04d1058 Mon Sep 17 00:00:00 2001
From: kolibril13 <44469195+kolibril13@users.noreply.github.com>
Date: Wed, 10 Nov 2021 12:58:18 +0100
Subject: [PATCH 05/21] removed helper scipt

---
 docs/source/hello.ipynb | 64 -----------------------------------------
 1 file changed, 64 deletions(-)
 delete mode 100644 docs/source/hello.ipynb

diff --git a/docs/source/hello.ipynb b/docs/source/hello.ipynb
deleted file mode 100644
index b935cc9b..00000000
--- a/docs/source/hello.ipynb
+++ /dev/null
@@ -1,64 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 7,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "/Users/jan-hendrik/projects/SimpleITK-Notebooks\n"
-     ]
-    }
-   ],
-   "source": [
-    "from pathlib import Path\n",
-    "import shutil\n",
-    "\n",
-    "ROOT_DIR = Path.cwd().parent.parent\n",
-    "print(ROOT_DIR )\n",
-    "\n",
-    "COPYFROM = ROOT_DIR \n",
-    "COPYTO = ROOT_DIR / \"docs\" / \"source\"\n",
-    "print(COPYFROM)\n",
-    "print(COPYTO)\n",
-    "folders = [\"Python\", \"Data\", \"Utilities\"]\n",
-    "for num, folder in enumerate(folders): \n",
-    "    print(\"######\")\n",
-    "    folder_from = COPYFROM/ folder\n",
-    "    folder_to = COPYTO /folder\n",
-    "    print(f\"{folder_from}\")\n",
-    "    print(f\"{folder_to}\")\n",
-    "    shutil.copytree(folder_from, folder_to)\n",
-    "    print(\"******DONE*******\")\n"
-   ]
-  }
- ],
- "metadata": {
-  "interpreter": {
-   "hash": "7ebf924f33491c921954fca832147f8f5cb2261a32d05c905747d88e8d31766a"
-  },
-  "kernelspec": {
-   "display_name": "Python 3.8.12 64-bit ('sitk': conda)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.12"
-  },
-  "orig_nbformat": 4
- },
- "nbformat": 4,
- "nbformat_minor": 2
-}

From dfce31b5796f9c1ad08c4aca91ff68dbb6b3e823 Mon Sep 17 00:00:00 2001
From: kolibril13 <44469195+kolibril13@users.noreply.github.com>
Date: Wed, 10 Nov 2021 13:08:54 +0100
Subject: [PATCH 06/21] make execution happen, fingers crossed again

---
 .gitignore          | 2 +-
 docs/source/conf.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitignore b/.gitignore
index eb47f27a..add0528d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,4 +11,4 @@ build
 .*.swp
 .mha
 .jpg
-docs/source/hello.ipynb # local helper script 
+docs/source/hello.ipynb
diff --git a/docs/source/conf.py b/docs/source/conf.py
index eff47205..382fc5f0 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -103,7 +103,7 @@
     'nbsphinx'
 ]
 nbsphinx_allow_errors = True
-nbsphinx_execute = 'never'
+#nbsphinx_execute = 'never'
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

From e1b00e2911dde2495d0d7a5d0811cadcdedaacd6 Mon Sep 17 00:00:00 2001
From: kolibril13 <44469195+kolibril13@users.noreply.github.com>
Date: Wed, 10 Nov 2021 13:52:13 +0100
Subject: [PATCH 07/21] try with more notebooks

---
 docs/source/conf.py              | 27 +++++++++++++++++++++------
 docs/source/delete_temp_files.py | 11 -----------
 2 files changed, 21 insertions(+), 17 deletions(-)
 delete mode 100644 docs/source/delete_temp_files.py

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 382fc5f0..10a39386 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -15,8 +15,24 @@
 # sys.path.insert(0, os.path.abspath('.'))
 
 # PreProcessing:
+
 from pathlib import Path
 import shutil
+
+## deleting all files in docs/source, when they should exist
+# DOCS_SOURCE_DIR = Path.cwd()  / "source"
+# print(DOCS_SOURCE_DIR)
+
+# folders = ["Python", "Data", "Utilities"]
+# for folder in folders:
+#     print(DOCS_SOURCE_DIR / folder)
+#     try:
+#         shutil.rmtree(DOCS_SOURCE_DIR/folder)
+#     except FileNotFoundError:
+#         print(f"Directory {DOCS_SOURCE_DIR/folder} was not yet in docs/source, so not deleted.")
+
+# Copy notebooks to source
+
 print("########################")
 print("########################")
 print("########################")
@@ -24,7 +40,6 @@
 
 ROOT_DIR = Path.cwd().parent.parent
 print(ROOT_DIR )
-# Copy notebooks to source
 COPYFROM = ROOT_DIR 
 COPYTO = ROOT_DIR / "docs" / "source"
 print(COPYFROM)
@@ -52,13 +67,13 @@
 "Python/11_Progress.ipynb",
 "Python/20_Expand_With_Interpolators.ipynb",
 "Python/21_Transforms_and_Resampling.ipynb",
-"Python/22_Transforms.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/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",
diff --git a/docs/source/delete_temp_files.py b/docs/source/delete_temp_files.py
deleted file mode 100644
index 440add46..00000000
--- a/docs/source/delete_temp_files.py
+++ /dev/null
@@ -1,11 +0,0 @@
-import shutil
-from pathlib import Path
-
-DOCS_SOURCE_DIR = Path.cwd()  / "source"
-print(DOCS_SOURCE_DIR)
-
-folders = ["Python", "Data", "Utilities"]
-for folder in folders:
-    print(DOCS_SOURCE_DIR / folder)
-    shutil.rmtree(DOCS_SOURCE_DIR/folder)
-

From a71bde51070365527633ccb20b9ef8aa9aab62e7 Mon Sep 17 00:00:00 2001
From: kolibril13 <44469195+kolibril13@users.noreply.github.com>
Date: Wed, 10 Nov 2021 14:04:30 +0100
Subject: [PATCH 08/21] more notebooks

---
 docs/source/conf.py | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 10a39386..6b2f9b10 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -63,28 +63,28 @@
 "Python/03_Image_Details.ipynb",
 "Python/04_Image_Display.ipynb",
 "Python/05_Results_Visualization.ipynb",
-#"Python/10_matplotlibs_imshow.ipynb",
+"Python/10_matplotlibs_imshow.ipynb",
 "Python/11_Progress.ipynb",
-"Python/20_Expand_With_Interpolators.ipynb",
-"Python/21_Transforms_and_Resampling.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/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/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",

From 9919bbf10d69c46da88faa4831150c702cbf90a8 Mon Sep 17 00:00:00 2001
From: kolibril13 <44469195+kolibril13@users.noreply.github.com>
Date: Wed, 10 Nov 2021 14:50:43 +0100
Subject: [PATCH 09/21] kernel died att 55, so removing that one

---
 docs/source/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 6b2f9b10..54d668a0 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -77,7 +77,7 @@
 #"Python/35_Segmentation_Shape_Analysis.ipynb",
 #"Python/36_Microscopy_Colocalization_Distance_Analysis.ipynb",
 #"Python/51_VH_Segmentation1.ipynb",
-#"Python/55_VH_Resample.ipynb",
+"Python/55_VH_Resample.ipynb",
 #"Python/56_VH_Registration1.ipynb",
 #"Python/60_Registration_Introduction.ipynb",
 #"Python/61_Registration_Introduction_Continued.ipynb",

From c29a1de745a829a76471b7f976f5a99fff82f566 Mon Sep 17 00:00:00 2001
From: kolibril13 <44469195+kolibril13@users.noreply.github.com>
Date: Wed, 10 Nov 2021 16:01:01 +0100
Subject: [PATCH 10/21] systematic testing

---
 docs/source/conf.py | 40 ++++++++++++++++++++--------------------
 1 file changed, 20 insertions(+), 20 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 54d668a0..c8b18578 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -63,28 +63,28 @@
 "Python/03_Image_Details.ipynb",
 "Python/04_Image_Display.ipynb",
 "Python/05_Results_Visualization.ipynb",
-"Python/10_matplotlibs_imshow.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/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/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",

From 0b96c537d5360662b781d3c3678a3a7dc50e7977 Mon Sep 17 00:00:00 2001
From: kolibril13 <44469195+kolibril13@users.noreply.github.com>
Date: Wed, 10 Nov 2021 16:02:04 +0100
Subject: [PATCH 11/21] remove extra line

---
 docs/source/conf.py | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index c8b18578..a55a2d3b 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -19,17 +19,6 @@
 from pathlib import Path
 import shutil
 
-## deleting all files in docs/source, when they should exist
-# DOCS_SOURCE_DIR = Path.cwd()  / "source"
-# print(DOCS_SOURCE_DIR)
-
-# folders = ["Python", "Data", "Utilities"]
-# for folder in folders:
-#     print(DOCS_SOURCE_DIR / folder)
-#     try:
-#         shutil.rmtree(DOCS_SOURCE_DIR/folder)
-#     except FileNotFoundError:
-#         print(f"Directory {DOCS_SOURCE_DIR/folder} was not yet in docs/source, so not deleted.")
 
 # Copy notebooks to source
 

From 02ce85c7274589f73f5823cf3e8ff7174f875321 Mon Sep 17 00:00:00 2001
From: kolibril13 <44469195+kolibril13@users.noreply.github.com>
Date: Wed, 10 Nov 2021 16:05:51 +0100
Subject: [PATCH 12/21] added more notebooks

---
 docs/source/conf.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index a55a2d3b..8bdf88b2 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -47,11 +47,11 @@
 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/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",

From 095e51186bbd7c8f0eb86528b0aeb151356c73fb Mon Sep 17 00:00:00 2001
From: kolibril13 <44469195+kolibril13@users.noreply.github.com>
Date: Wed, 10 Nov 2021 16:26:08 +0100
Subject: [PATCH 13/21] adding 11

---
 docs/source/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 8bdf88b2..990a695e 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -53,7 +53,7 @@
 #"Python/04_Image_Display.ipynb",
 #"Python/05_Results_Visualization.ipynb",
 #"Python/10_matplotlibs_imshow.ipynb",
-"Python/11_Progress.ipynb",
+#"Python/11_Progress.ipynb",
 "Python/20_Expand_With_Interpolators.ipynb",
 "Python/21_Transforms_and_Resampling.ipynb",
 "Python/22_Transforms.ipynb",

From 510eb1fe42614c51d2603dbb3f01d54bf920810c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan-Hendrik=20M=C3=BCller?=
 <44469195+kolibril13@users.noreply.github.com>
Date: Mon, 15 Nov 2021 19:10:09 +0100
Subject: [PATCH 14/21] empty commit to re-trigger rdt

---
 docs/source/index.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/index.rst b/docs/source/index.rst
index 6de7bd33..e87f9db8 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -48,7 +48,7 @@ Contents can be used for:
     Python/70_Data_Augmentation.ipynb
     Python/71_Trust_But_Verify.ipynb
 
-
+ 
 
 Repository on GitHub:
 https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks
\ No newline at end of file

From 5f9bf139967cf98fad1d1e6eb851243e693dd19a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan-Hendrik=20M=C3=BCller?=
 <44469195+kolibril13@users.noreply.github.com>
Date: Mon, 15 Nov 2021 19:56:42 +0100
Subject: [PATCH 15/21] change nbsphinx_timeout value

---
 docs/source/conf.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 990a695e..fa053404 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -106,6 +106,7 @@
     'sphinx_copybutton',
     'nbsphinx'
 ]
+nbsphinx_timeout = 10000 
 nbsphinx_allow_errors = True
 #nbsphinx_execute = 'never'
 

From 00ca8e5c46f77bd285f00b25d90817a5b284cd2a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan-Hendrik=20M=C3=BCller?=
 <44469195+kolibril13@users.noreply.github.com>
Date: Mon, 15 Nov 2021 20:10:35 +0100
Subject: [PATCH 16/21] added even more notebooks

---
 docs/source/conf.py | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index fa053404..1432f4da 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -54,17 +54,17 @@
 #"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/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",

From 289a0c4ceca66852cb0b366a0fdf5f29d13df75c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan-Hendrik=20M=C3=BCller?=
 <44469195+kolibril13@users.noreply.github.com>
Date: Mon, 15 Nov 2021 22:24:52 +0100
Subject: [PATCH 17/21] adding more notebooks

---
 docs/source/conf.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 1432f4da..712b0d57 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -65,15 +65,15 @@
 #"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/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",

From c02dbb57cf916f0fbb9ab0cd2ea589fb83e97ff0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan-Hendrik=20M=C3=BCller?=
 <44469195+kolibril13@users.noreply.github.com>
Date: Mon, 15 Nov 2021 22:47:18 +0100
Subject: [PATCH 18/21] removing 11_Progress

---
 docs/source/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 712b0d57..29c5020b 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -53,7 +53,7 @@
 #"Python/04_Image_Display.ipynb",
 #"Python/05_Results_Visualization.ipynb",
 #"Python/10_matplotlibs_imshow.ipynb",
-#"Python/11_Progress.ipynb",
+"Python/11_Progress.ipynb",
 #"Python/20_Expand_With_Interpolators.ipynb",
 #"Python/21_Transforms_and_Resampling.ipynb",
 #"Python/22_Transforms.ipynb",

From e15bc24579729c970742a17643c31b0788a49f9b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan-Hendrik=20M=C3=BCller?=
 <44469195+kolibril13@users.noreply.github.com>
Date: Mon, 15 Nov 2021 23:33:24 +0100
Subject: [PATCH 19/21] remove 55

---
 docs/source/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 29c5020b..e563e50a 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -66,7 +66,7 @@
 #"Python/35_Segmentation_Shape_Analysis.ipynb",
 #"Python/36_Microscopy_Colocalization_Distance_Analysis.ipynb",
 #"Python/51_VH_Segmentation1.ipynb",
-#"Python/55_VH_Resample.ipynb",
+"Python/55_VH_Resample.ipynb",
 #"Python/56_VH_Registration1.ipynb",
 #"Python/60_Registration_Introduction.ipynb",
 #"Python/61_Registration_Introduction_Continued.ipynb",

From 8683523b18c0d3bff266b829926e226327077a35 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan-Hendrik=20M=C3=BCller?=
 <44469195+kolibril13@users.noreply.github.com>
Date: Tue, 16 Nov 2021 00:21:31 +0100
Subject: [PATCH 20/21] remove some registration notebooks

---
 docs/source/conf.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index e563e50a..c041cda7 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -71,9 +71,9 @@
 #"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/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",

From 612918276c7d9a1db030e2886e193016cf3a494c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan-Hendrik=20M=C3=BCller?=
 <44469195+kolibril13@users.noreply.github.com>
Date: Tue, 16 Nov 2021 09:20:36 +0100
Subject: [PATCH 21/21] added more notebooks

---
 docs/source/conf.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index c041cda7..336c4c56 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -71,15 +71,15 @@
 #"Python/60_Registration_Introduction.ipynb",
 #"Python/61_Registration_Introduction_Continued.ipynb",
 #"Python/62_Registration_Tuning.ipynb",
-"Python/63_Registration_Initialization.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",
+#"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: