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diff --git a/documentation/_build/doctrees/WorkSchedule_2019.doctree b/documentation/_build/doctrees/WorkSchedule_2019.doctree
diff --git a/documentation/_build/doctrees/api/app_from_img_to_categories.doctree b/documentation/_build/doctrees/api/app_from_img_to_categories.doctree
diff --git a/documentation/_build/doctrees/api/combine_labels.doctree b/documentation/_build/doctrees/api/combine_labels.doctree
diff --git a/documentation/_build/doctrees/api/echo.doctree b/documentation/_build/doctrees/api/echo.doctree
diff --git a/documentation/_build/doctrees/api/feature_extraction.doctree b/documentation/_build/doctrees/api/feature_extraction.doctree
diff --git a/documentation/_build/doctrees/api/get_valid_triples.doctree b/documentation/_build/doctrees/api/get_valid_triples.doctree
diff --git a/documentation/_build/doctrees/api/good_style.doctree b/documentation/_build/doctrees/api/good_style.doctree
diff --git a/documentation/_build/doctrees/api/labelCNN.doctree b/documentation/_build/doctrees/api/labelCNN.doctree
diff --git a/documentation/_build/doctrees/api/label_app.doctree b/documentation/_build/doctrees/api/label_app.doctree
diff --git a/documentation/_build/doctrees/api/measure_agreement.doctree b/documentation/_build/doctrees/api/measure_agreement.doctree
diff --git a/documentation/_build/doctrees/api/modules.doctree b/documentation/_build/doctrees/api/modules.doctree
diff --git a/documentation/_build/doctrees/api/move_files.doctree b/documentation/_build/doctrees/api/move_files.doctree
diff --git a/documentation/_build/doctrees/api/perform_preprocessing.doctree b/documentation/_build/doctrees/api/perform_preprocessing.doctree
diff --git a/documentation/_build/doctrees/api/pipeline.doctree b/documentation/_build/doctrees/api/pipeline.doctree
diff --git a/documentation/_build/doctrees/api/plot_agreement_data.doctree b/documentation/_build/doctrees/api/plot_agreement_data.doctree
diff --git a/documentation/_build/doctrees/api/preprocess.doctree b/documentation/_build/doctrees/api/preprocess.doctree
diff --git a/documentation/_build/doctrees/api/preprocess_BACKUP_1045.doctree b/documentation/_build/doctrees/api/preprocess_BACKUP_1045.doctree
diff --git a/documentation/_build/doctrees/api/preprocess_BASE_1045.doctree b/documentation/_build/doctrees/api/preprocess_BASE_1045.doctree
diff --git a/documentation/_build/doctrees/api/preprocess_LOCAL_1045.doctree b/documentation/_build/doctrees/api/preprocess_LOCAL_1045.doctree
diff --git a/documentation/_build/doctrees/api/preprocess_REMOTE_1045.doctree b/documentation/_build/doctrees/api/preprocess_REMOTE_1045.doctree
diff --git a/documentation/_build/doctrees/api/preprocess_locally.doctree b/documentation/_build/doctrees/api/preprocess_locally.doctree
diff --git a/documentation/_build/doctrees/api/preprocessor.doctree b/documentation/_build/doctrees/api/preprocessor.doctree
diff --git a/documentation/_build/doctrees/api/preprocessor_BACKUP_470.doctree b/documentation/_build/doctrees/api/preprocessor_BACKUP_470.doctree
diff --git a/documentation/_build/doctrees/api/preprocessor_BASE_470.doctree b/documentation/_build/doctrees/api/preprocessor_BASE_470.doctree
diff --git a/documentation/_build/doctrees/api/preprocessor_LOCAL_470.doctree b/documentation/_build/doctrees/api/preprocessor_LOCAL_470.doctree
diff --git a/documentation/_build/doctrees/api/preprocessor_REMOTE_470.doctree b/documentation/_build/doctrees/api/preprocessor_REMOTE_470.doctree
diff --git a/documentation/_build/doctrees/api/stack_images.doctree b/documentation/_build/doctrees/api/stack_images.doctree
diff --git a/documentation/_build/doctrees/api/start_preprocessing.doctree b/documentation/_build/doctrees/api/start_preprocessing.doctree
diff --git a/documentation/_build/doctrees/api/start_preprocessing2.doctree b/documentation/_build/doctrees/api/start_preprocessing2.doctree
diff --git a/documentation/_build/doctrees/api/submit_script.doctree b/documentation/_build/doctrees/api/submit_script.doctree
diff --git a/documentation/_build/doctrees/api/utils.doctree b/documentation/_build/doctrees/api/utils.doctree
diff --git a/documentation/_build/doctrees/api_docs.doctree b/documentation/_build/doctrees/api_docs.doctree
diff --git a/documentation/_build/doctrees/environment.pickle b/documentation/_build/doctrees/environment.pickle
diff --git a/documentation/_build/doctrees/index.doctree b/documentation/_build/doctrees/index.doctree
diff --git a/documentation/_build/doctrees/manuals.doctree b/documentation/_build/doctrees/manuals.doctree
diff --git a/documentation/_build/doctrees/manuals/manual_CONDA.doctree b/documentation/_build/doctrees/manuals/manual_CONDA.doctree
diff --git a/documentation/_build/doctrees/manuals/manual_dataSet.doctree b/documentation/_build/doctrees/manuals/manual_dataSet.doctree
diff --git a/documentation/_build/doctrees/manuals/manual_how_to_label.doctree b/documentation/_build/doctrees/manuals/manual_how_to_label.doctree
diff --git a/documentation/_build/doctrees/manuals/manual_latex.doctree b/documentation/_build/doctrees/manuals/manual_latex.doctree
diff --git a/documentation/_build/doctrees/manuals/manual_run_labelapp_externally.doctree b/documentation/_build/doctrees/manuals/manual_run_labelapp_externally.doctree
diff --git a/documentation/_build/doctrees/manuals/manual_run_streamlit_app.doctree b/documentation/_build/doctrees/manuals/manual_run_streamlit_app.doctree
diff --git a/documentation/_build/doctrees/paper_library.doctree b/documentation/_build/doctrees/paper_library.doctree
diff --git a/documentation/_build/doctrees/paper_library/paper_summary.doctree b/documentation/_build/doctrees/paper_library/paper_summary.doctree
diff --git a/documentation/_build/doctrees/protocols.doctree b/documentation/_build/doctrees/protocols.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_19_04_08.doctree b/documentation/_build/doctrees/protocols/protocol_19_04_08.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_19_04_12.doctree b/documentation/_build/doctrees/protocols/protocol_19_04_12.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_19_04_26.doctree b/documentation/_build/doctrees/protocols/protocol_19_04_26.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_19_05_03.doctree b/documentation/_build/doctrees/protocols/protocol_19_05_03.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_19_05_10.doctree b/documentation/_build/doctrees/protocols/protocol_19_05_10.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_19_05_17.doctree b/documentation/_build/doctrees/protocols/protocol_19_05_17.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_19_05_24.doctree b/documentation/_build/doctrees/protocols/protocol_19_05_24.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_19_05_31.doctree b/documentation/_build/doctrees/protocols/protocol_19_05_31.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_19_06_07.doctree b/documentation/_build/doctrees/protocols/protocol_19_06_07.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_19_06_14.doctree b/documentation/_build/doctrees/protocols/protocol_19_06_14.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_19_06_21.doctree b/documentation/_build/doctrees/protocols/protocol_19_06_21.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_19_06_28.doctree b/documentation/_build/doctrees/protocols/protocol_19_06_28.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_19_07_05.doctree b/documentation/_build/doctrees/protocols/protocol_19_07_05.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_19_09_06.doctree b/documentation/_build/doctrees/protocols/protocol_19_09_06.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_19_09_12.doctree b/documentation/_build/doctrees/protocols/protocol_19_09_12.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_19_11_15.doctree b/documentation/_build/doctrees/protocols/protocol_19_11_15.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_19_12_06.doctree b/documentation/_build/doctrees/protocols/protocol_19_12_06.doctree
diff --git a/documentation/_build/doctrees/protocols/protocol_initial_questions.doctree b/documentation/_build/doctrees/protocols/protocol_initial_questions.doctree
diff --git a/documentation/_build/doctrees/report.doctree b/documentation/_build/doctrees/report.doctree
diff --git a/documentation/_build/doctrees/report/README.doctree b/documentation/_build/doctrees/report/README.doctree
diff --git a/documentation/_build/doctrees/report/chapter_1_todo.doctree b/documentation/_build/doctrees/report/chapter_1_todo.doctree
diff --git a/documentation/_build/doctrees/report/chapter_2_todo.doctree b/documentation/_build/doctrees/report/chapter_2_todo.doctree
diff --git a/documentation/_build/doctrees/report/chapter_3_todo.doctree b/documentation/_build/doctrees/report/chapter_3_todo.doctree
diff --git a/documentation/_build/doctrees/report/chapter_4_todo.doctree b/documentation/_build/doctrees/report/chapter_4_todo.doctree
diff --git a/documentation/_build/doctrees/report/chapter_5_todo.doctree b/documentation/_build/doctrees/report/chapter_5_todo.doctree
diff --git a/documentation/_build/doctrees/report/chapter_6_todo.doctree b/documentation/_build/doctrees/report/chapter_6_todo.doctree
diff --git a/documentation/_build/doctrees/report/report_overview.doctree b/documentation/_build/doctrees/report/report_overview.doctree
diff --git a/documentation/_build/doctrees/workschedules.doctree b/documentation/_build/doctrees/workschedules.doctree
diff --git a/documentation/_build/html/.buildinfo b/documentation/_build/html/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 6a716e7e47665558de92b995555f062d
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/documentation/_build/html/WorkSchedule_2019.html b/documentation/_build/html/WorkSchedule_2019.html
diff --git a/documentation/_build/html/_sources/WorkSchedule_2019.md.txt b/documentation/_build/html/_sources/WorkSchedule_2019.md.txt
@@ -0,0 +1,95 @@
+# Workschedule 2019
+
+  -------------------------------------------------------------------------------------------------------------------------------------------------
+                            Josefine     Katha            Malin            Maren          Michael         Sophia          Subir        Richard
+  ------------ ------------ ------------ ---------------- ---------------- -------------- --------------- --------------- ------------ ------------
+  von          bis                                                                                                                     
+
+  02.11.2019   08.11.2019   label 300    label 300        label 300        label 300      Label 300       label 300       label 300    label 300
+                            pictures     pictures         pictures         pictures       pictures        pictures        pictures     pictures
+
+                            \- install   \- install       \- install       \- install     \- label app    \- install      \-           \- install
+                            labelapp     labelapp         labelapp\        labelapp\      manager\        labelapp\                    labelapp\
+                                                          - edit manual    - addition 200 - changed       - pre-processor              - Datenset
+                                                          labelapp\        images         pre-processor   kappa 3h\                    5h\
+                                                          - pre-processor  labelled       app\            - Work                       - Work
+                                                          kappa 3h                        - improved      schedule\                    schedule\
+                                                                                          labelapp        - pre-processor              - how to
+                                                                                                          app                          install
+                                                                                                                                       labelapp
+
+  09.11.2019   15.11.2019   label 500    label 500        label 500        label 500      label 500       label 500       label 500    label 500
+                            pictures     pictures         pictures         pictures       pictures        pictures        pictures\    pictures
+                                                                                                                          label        
+                                                                                                                          additional   
+                                                                                                                          500          
+
+                            \- report    \- get healthy   \- kappa &       \- csv file    \- label app    \- finish                    \- env
+                            manager\     100h             visualisation    manager\       manager\        pre-processor                manager\
+                            - write                       for report (and  - test label   - finish        4h\                          - create
+                            report 8h\                    presentation?)   app, report    pre-processor   - classical                  dataset 8h
+                            - transfer                    8h               all possible   4h\             approach                     
+                            all                                            bugs 5h\       - fix           (features to                 
+                            googledocs                                     - control all  eventually bug  classes)                     
+                            to github                                      label          / test app 4h                                
+                                                                           activities 3h\                                              
+                                                                           - assign                                                    
+                                                                           images to be                                                
+                                                                           labelled 1h                                                 
+
+  16.11.2019   22.11.2019   label 500    label 500        label 500        label 500      label 500       label 500       label 500    label 500
+                            pictures     pictures         pictures         pictures       pictures        pictures        pictures     pictures
+
+                            \- report    \- get healthy   \- look at       \- csv file    \- label app    \- look at                   \- env
+                            manager\     100h             labels, feature  manager\       manager\        labels, feature              manager\
+                            - write                       distribution,    - file         - grid manager\ distribution,                - create
+                            report 8h                     compare to       controller 2h\ - fix           compare to                   dataset 8h
+                                                          assigned class,  - write report eventually bug  assigned class,              
+                                                          decision tree?   6h             / test app 4h\  decision tree?               
+                                                          8h                              - grid how to   8h                           
+                                                                                          use manual                                   
+
+  23.11.2019   29.11.2019   label 500    label 500        label 500        label 500      label 500       label 500       label 500    label 500
+                            pictures     pictures         pictures         pictures       pictures        pictures        pictures     pictures
+
+                            \- report    \- github        \- ANN manager\  \- csv file    \- grid         \- final report              \- finalize
+                            manager\     manager\         - unsupervised   manager\       manager\        for: look at                 dataset 4h\
+                            - Vanilla    - transfer       learning         - unsupervised - label app     labels, feature              - Vanilla
+                            CNN 8h       Images & Dataset                  learning       manager         distribution,                CNN\
+                                         to                                                               compare to                   - env
+                                         wintersemester                                                   assigned class,              manager
+                                         (clean cut)\                                                     decision tree?               
+                                         - how to deal                                                    4h\                          
+                                         with different                                                   - Vanilla CNN                
+                                         ANN-files                                                        4h                           
+
+  30.11.2019   06.12.2019   label 500    label 500        label 500        label 500      label 500       label 500       label 500    label 500
+                            pictures     pictures         pictures         pictures       pictures        pictures        pictures     pictures
+
+                            \- report    \- github        \- ANN manager\  \- csv file    \- grid         \- semi                      \- semi
+                            manager\     manager          - unsupervised   manager\       manager\        supervised                   supervised
+                            - Vanilla                     learning         - unsupervised - label app     learning                     learning
+                            CNN 8h                                         learning       manager                                      
+
+  07.12.2019   13.12.2019   label 500    label 500        label 500        label 500      label 500       label 500       label 500    label 500
+                            pictures     pictures         pictures         pictures       pictures        pictures        pictures     pictures
+
+                            \- report    \- github        \- ANN manager\  \- csv file    \- grid         \- get ANN task              \- get ANN
+                            manager\     manager\         - get ANN task   manager\       manager\        from ANN                     task from
+                            - get ANN    - get ANN task   from ANN manager - get ANN task - label app     manager                      ANN manager
+                            task from    from ANN manager                  from ANN       manager\                                     
+                            ANN manager                                    manager        - get ANN task                               
+                                                                                          from ANN                                     
+                                                                                          manager                                      
+
+  14.12.2019   20.12.2019   label 500    label 500        label 500        label 500      label 500       label 500       label 500    label 500
+                            pictures     pictures         pictures         pictures       pictures        pictures        pictures     pictures
+
+                            \- report    \- github        \- ANN manager\  \- csv file    \- grid         \- get ANN task              \- get ANN
+                            manager\     manager\         - get ANN task   manager\       manager\        from ANN                     task from
+                            - get ANN    - get ANN task   from ANN manager - get ANN task - label app     manager                      ANN manager
+                            task from    from ANN manager                  from ANN       manager\                                     
+                            ANN manager                                    manager        - get ANN task                               
+                                                                                          from ANN                                     
+                                                                                          manager                                      
+  -------------------------------------------------------------------------------------------------------------------------------------------------
diff --git a/...tation/api/app_from_img_to_categories.rst → ...es/api/app_from_img_to_categories.rst.txt b/...tation/api/app_from_img_to_categories.rst → ...es/api/app_from_img_to_categories.rst.txt
diff --git a/documentation/api/combine_labels.rst → .../html/_sources/api/combine_labels.rst.txt b/documentation/api/combine_labels.rst → .../html/_sources/api/combine_labels.rst.txt
diff --git a/documentation/_build/html/_sources/api/echo.rst.txt b/documentation/_build/html/_sources/api/echo.rst.txt
@@ -0,0 +1,7 @@
+echo module
+===========
+
+.. automodule:: echo
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/feature_extraction.rst.txt b/documentation/_build/html/_sources/api/feature_extraction.rst.txt
@@ -0,0 +1,7 @@
+feature\_extraction module
+==========================
+
+.. automodule:: feature_extraction
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/get_valid_triples.rst.txt b/documentation/_build/html/_sources/api/get_valid_triples.rst.txt
@@ -0,0 +1,7 @@
+get\_valid\_triples module
+==========================
+
+.. automodule:: get_valid_triples
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/api/good_style.rst → ...uild/html/_sources/api/good_style.rst.txt b/documentation/api/good_style.rst → ...uild/html/_sources/api/good_style.rst.txt
diff --git a/documentation/api/labelCNN.rst → ..._build/html/_sources/api/labelCNN.rst.txt b/documentation/api/labelCNN.rst → ..._build/html/_sources/api/labelCNN.rst.txt
diff --git a/documentation/_build/html/_sources/api/label_app.rst.txt b/documentation/_build/html/_sources/api/label_app.rst.txt
@@ -0,0 +1,7 @@
+label\_app module
+=================
+
+.. automodule:: label_app
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/api/measure_agreement.rst → ...ml/_sources/api/measure_agreement.rst.txt b/documentation/api/measure_agreement.rst → ...ml/_sources/api/measure_agreement.rst.txt
diff --git a/documentation/_build/html/_sources/api/modules.rst.txt b/documentation/_build/html/_sources/api/modules.rst.txt
@@ -0,0 +1,28 @@
+preprocessing
+=============
+
+.. toctree::
+   :maxdepth: 4
+
+   echo
+   feature_extraction
+   get_valid_triples
+   label_app
+   move_files
+   perform_preprocessing
+   preprocess
+   preprocess_BACKUP_1045
+   preprocess_BASE_1045
+   preprocess_LOCAL_1045
+   preprocess_REMOTE_1045
+   preprocess_locally
+   preprocessor
+   preprocessor_BACKUP_470
+   preprocessor_BASE_470
+   preprocessor_LOCAL_470
+   preprocessor_REMOTE_470
+   stack_images
+   start_preprocessing
+   start_preprocessing2
+   submit_script
+   utils
diff --git a/documentation/_build/html/_sources/api/move_files.rst.txt b/documentation/_build/html/_sources/api/move_files.rst.txt
@@ -0,0 +1,7 @@
+move\_files module
+==================
+
+.. automodule:: move_files
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/perform_preprocessing.rst.txt b/documentation/_build/html/_sources/api/perform_preprocessing.rst.txt
@@ -0,0 +1,7 @@
+perform\_preprocessing module
+=============================
+
+.. automodule:: perform_preprocessing
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/api/pipeline.rst → ..._build/html/_sources/api/pipeline.rst.txt b/documentation/api/pipeline.rst → ..._build/html/_sources/api/pipeline.rst.txt
diff --git a/documentation/api/plot_agreement_data.rst → .../_sources/api/plot_agreement_data.rst.txt b/documentation/api/plot_agreement_data.rst → .../_sources/api/plot_agreement_data.rst.txt
diff --git a/documentation/_build/html/_sources/api/preprocess.rst.txt b/documentation/_build/html/_sources/api/preprocess.rst.txt
@@ -0,0 +1,7 @@
+preprocess module
+=================
+
+.. automodule:: preprocess
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/preprocess_BACKUP_1045.rst.txt b/documentation/_build/html/_sources/api/preprocess_BACKUP_1045.rst.txt
@@ -0,0 +1,7 @@
+preprocess\_BACKUP\_1045 module
+===============================
+
+.. automodule:: preprocess_BACKUP_1045
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/preprocess_BASE_1045.rst.txt b/documentation/_build/html/_sources/api/preprocess_BASE_1045.rst.txt
@@ -0,0 +1,7 @@
+preprocess\_BASE\_1045 module
+=============================
+
+.. automodule:: preprocess_BASE_1045
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/preprocess_LOCAL_1045.rst.txt b/documentation/_build/html/_sources/api/preprocess_LOCAL_1045.rst.txt
@@ -0,0 +1,7 @@
+preprocess\_LOCAL\_1045 module
+==============================
+
+.. automodule:: preprocess_LOCAL_1045
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/preprocess_REMOTE_1045.rst.txt b/documentation/_build/html/_sources/api/preprocess_REMOTE_1045.rst.txt
@@ -0,0 +1,7 @@
+preprocess\_REMOTE\_1045 module
+===============================
+
+.. automodule:: preprocess_REMOTE_1045
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/preprocess_locally.rst.txt b/documentation/_build/html/_sources/api/preprocess_locally.rst.txt
@@ -0,0 +1,7 @@
+preprocess\_locally module
+==========================
+
+.. automodule:: preprocess_locally
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/preprocessor.rst.txt b/documentation/_build/html/_sources/api/preprocessor.rst.txt
@@ -0,0 +1,7 @@
+preprocessor module
+===================
+
+.. automodule:: preprocessor
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/preprocessor_BACKUP_470.rst.txt b/documentation/_build/html/_sources/api/preprocessor_BACKUP_470.rst.txt
@@ -0,0 +1,7 @@
+preprocessor\_BACKUP\_470 module
+================================
+
+.. automodule:: preprocessor_BACKUP_470
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/preprocessor_BASE_470.rst.txt b/documentation/_build/html/_sources/api/preprocessor_BASE_470.rst.txt
@@ -0,0 +1,7 @@
+preprocessor\_BASE\_470 module
+==============================
+
+.. automodule:: preprocessor_BASE_470
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/preprocessor_LOCAL_470.rst.txt b/documentation/_build/html/_sources/api/preprocessor_LOCAL_470.rst.txt
@@ -0,0 +1,7 @@
+preprocessor\_LOCAL\_470 module
+===============================
+
+.. automodule:: preprocessor_LOCAL_470
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/preprocessor_REMOTE_470.rst.txt b/documentation/_build/html/_sources/api/preprocessor_REMOTE_470.rst.txt
@@ -0,0 +1,7 @@
+preprocessor\_REMOTE\_470 module
+================================
+
+.. automodule:: preprocessor_REMOTE_470
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/stack_images.rst.txt b/documentation/_build/html/_sources/api/stack_images.rst.txt
@@ -0,0 +1,7 @@
+stack\_images module
+====================
+
+.. automodule:: stack_images
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/start_preprocessing.rst.txt b/documentation/_build/html/_sources/api/start_preprocessing.rst.txt
@@ -0,0 +1,7 @@
+start\_preprocessing module
+===========================
+
+.. automodule:: start_preprocessing
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/start_preprocessing2.rst.txt b/documentation/_build/html/_sources/api/start_preprocessing2.rst.txt
@@ -0,0 +1,7 @@
+start\_preprocessing2 module
+============================
+
+.. automodule:: start_preprocessing2
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/submit_script.rst.txt b/documentation/_build/html/_sources/api/submit_script.rst.txt
@@ -0,0 +1,7 @@
+submit\_script module
+=====================
+
+.. automodule:: submit_script
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api/utils.rst.txt b/documentation/_build/html/_sources/api/utils.rst.txt
@@ -0,0 +1,7 @@
+utils module
+============
+
+.. automodule:: utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/_build/html/_sources/api_docs.rst.txt b/documentation/_build/html/_sources/api_docs.rst.txt
@@ -0,0 +1,9 @@
+API Documentation
+=================
+
+.. toctree::
+   :maxdepth: 6
+   :caption: API Documentation:
+   :glob:
+
+   api/modules
diff --git a/documentation/_build/html/_sources/index.rst.txt b/documentation/_build/html/_sources/index.rst.txt
@@ -0,0 +1,26 @@
+.. asparagus documentation master file, created by
+   sphinx-quickstart on Mon Jun  3 00:34:49 2019.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to asparagus's documentation!
+=====================================
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Contents:
+
+   protocols.rst
+   report.rst
+   workschedules.rst
+   manuals.rst
+   api_docs.rst
+   paper_library.rst
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
diff --git a/documentation/_build/html/_sources/manuals.rst.txt b/documentation/_build/html/_sources/manuals.rst.txt
@@ -0,0 +1,9 @@
+Manuals
+==============
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Manuals:
+   :glob:
+
+   manuals/*
diff --git a/documentation/_build/html/_sources/manuals/manual_CONDA.md.txt b/documentation/_build/html/_sources/manuals/manual_CONDA.md.txt
@@ -0,0 +1,42 @@
+# Get hands on - use shared conda installation
+To use the shared installation you have to tell linux where it is.
+1. Log in
+    `ssh [email protected]`
+2. Add some lines at the end of your bashrc file: </br>
+    `$ nano -Bu ~/.bashrc` </br> 
+    Or you could use ranger or vim instead...</br>
+    ```
+    # >>> conda initialize >>>
+    # !! Contents within this block are managed by 'conda init' !!
+    __conda_setup="$('/net/projects/scratch/winter/valid_until_31_July_2020/asparagus/sharedConda/bin/conda' 'shell.bash' '$if [ $? -eq 0 ]; then
+        eval "$__conda_setup"
+    else
+        if [ -f "/net/projects/scratch/winter/valid_until_31_July_2020/asparagus/sharedConda/etc/profile.d/conda.sh" ]; then        . "/net/projects/scratch/winter/        valid_until_31_July_2020/asparagus/sharedConda/etc/profile.d/conda.sh"
+        else
+        export PATH="/net/projects/scratch/winter/valid_until_31_July_2020/asparagus/sharedConda/bin:$PATH"
+        fi
+    fi
+    unset __conda_setup
+    # <<< conda initialize <<<
+    ```
+
+
+3. For changes to take effect, close and re-open your current shell.</br>
+    `$ exit` 
+4. Log in again. If you want to use a single GPU log in to shadow or light.
+    You can test it with:
+    `$ nvidia-smi`
+4. If you prefer that condas base environment is not activated on startup,</br>
+    set the auto_activate_base parameter to false:</br>
+    `$ conda config --set auto_activate_base false`
+5. After Log in hit: </br>
+
+    `$ conda activate dataSet`
+    or
+     `$ conda activate /net/projects/scratch/winter/valid_until_31_July_2020/asparagus/sharedConda/envs/dataSet/`
+ 6. Test a tensorflow file on the GPU</br>
+    `$ nvidia-smi -l`
+
+
+Check this link out, if you want to know more about shared installations:
+https://docs.anaconda.com/anaconda/install/multi-user/