From 70aae27e6ad5282489dd28fb2fb057cc3614add2 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Tue, 5 Nov 2019 10:47:41 +0100
Subject: [PATCH] Move registration/9.9.9 to registration/deprecated
---
registration/0.5.4/README.txt | 2 --
.../{9.9.9 => deprecated}/EM/nuclei_to_remove.csv | 0
.../EM/nucleus_exclusion_mask.xml | 0
.../notes/registration-strategy.txt | 0
.../compute-registration-quality.R | 0
.../quality-assessment/em-fixed-points.txt | 0
.../quality-assessment/manually_matched_points.xlsx | Bin
.../quality-assessment/notes.txt | 0
.../quality-assessment/outputpoints.txt | 0
.../quality-assessment/transformix.log | Bin
.../~$manually_matched_points.xlsx | Bin
.../{9.9.9 => deprecated}/scripts/elastix.ijm | 0
.../scripts/mask_gut_nuclei.py | 0
.../scripts/prepare_image_data.ijm | 0
.../exclude_nuclei_from_table.py | 0
.../scripts/registration_targets/move_meds.py | 0
.../scripts/registration_targets/set_voxel_size.ijm | 0
.../stomach_registration_targets.py | 0
.../transfer_ProSPr_data/ProSPr_copy_and_mirror.ijm | 0
.../transfer_ProSPr_data/ProSPr_copy_and_mirror.sh | 0
.../TransformParameters.BSpline10.9.9.9.txt | 0
.../TransformParameters.BSpline100.9.9.9.txt | 0
.../TransformParameters.BSpline30.9.9.9.txt | 0
.../TransformParameters.RotationPreAlign.0.0.0.txt | 0
.../TransformParameters.Similarity.0.0.0.txt | 0
.../TransformParameters.Similarity.0.txt | 0
.../TransformParameters.Similarity.9.9.9.txt | 0
27 files changed, 2 deletions(-)
delete mode 100644 registration/0.5.4/README.txt
rename registration/{9.9.9 => deprecated}/EM/nuclei_to_remove.csv (100%)
rename registration/{9.9.9 => deprecated}/EM/nucleus_exclusion_mask.xml (100%)
rename registration/{9.9.9 => deprecated}/notes/registration-strategy.txt (100%)
rename registration/{9.9.9 => deprecated}/quality-assessment/compute-registration-quality.R (100%)
rename registration/{9.9.9 => deprecated}/quality-assessment/em-fixed-points.txt (100%)
rename registration/{9.9.9 => deprecated}/quality-assessment/manually_matched_points.xlsx (100%)
rename registration/{9.9.9 => deprecated}/quality-assessment/notes.txt (100%)
rename registration/{9.9.9 => deprecated}/quality-assessment/outputpoints.txt (100%)
rename registration/{9.9.9 => deprecated}/quality-assessment/transformix.log (100%)
rename registration/{9.9.9 => deprecated}/quality-assessment/~$manually_matched_points.xlsx (100%)
rename registration/{9.9.9 => deprecated}/scripts/elastix.ijm (100%)
rename registration/{9.9.9 => deprecated}/scripts/mask_gut_nuclei.py (100%)
rename registration/{9.9.9 => deprecated}/scripts/prepare_image_data.ijm (100%)
rename registration/{9.9.9 => deprecated}/scripts/registration_targets/exclude_nuclei_from_table.py (100%)
rename registration/{9.9.9 => deprecated}/scripts/registration_targets/move_meds.py (100%)
rename registration/{9.9.9 => deprecated}/scripts/registration_targets/set_voxel_size.ijm (100%)
rename registration/{9.9.9 => deprecated}/scripts/registration_targets/stomach_registration_targets.py (100%)
rename registration/{9.9.9 => deprecated}/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.ijm (100%)
rename registration/{9.9.9 => deprecated}/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.sh (100%)
rename registration/{9.9.9 => deprecated}/transformations/TransformParameters.BSpline10.9.9.9.txt (100%)
rename registration/{9.9.9 => deprecated}/transformations/TransformParameters.BSpline100.9.9.9.txt (100%)
rename registration/{9.9.9 => deprecated}/transformations/TransformParameters.BSpline30.9.9.9.txt (100%)
rename registration/{9.9.9 => deprecated}/transformations/TransformParameters.RotationPreAlign.0.0.0.txt (100%)
rename registration/{9.9.9 => deprecated}/transformations/TransformParameters.Similarity.0.0.0.txt (100%)
rename registration/{9.9.9 => deprecated}/transformations/TransformParameters.Similarity.0.txt (100%)
rename registration/{9.9.9 => deprecated}/transformations/TransformParameters.Similarity.9.9.9.txt (100%)
diff --git a/registration/0.5.4/README.txt b/registration/0.5.4/README.txt
deleted file mode 100644
index f48879c..0000000
--- a/registration/0.5.4/README.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-Registration based only on nuclei/dapi. I got this from Tischi and I am not quite sure if these transformations correspond to '9.9.9/transformations'.
-Replace this folder with 9.9.9, if transformations turn out to be identical.
diff --git a/registration/9.9.9/EM/nuclei_to_remove.csv b/registration/deprecated/EM/nuclei_to_remove.csv
similarity index 100%
rename from registration/9.9.9/EM/nuclei_to_remove.csv
rename to registration/deprecated/EM/nuclei_to_remove.csv
diff --git a/registration/9.9.9/EM/nucleus_exclusion_mask.xml b/registration/deprecated/EM/nucleus_exclusion_mask.xml
similarity index 100%
rename from registration/9.9.9/EM/nucleus_exclusion_mask.xml
rename to registration/deprecated/EM/nucleus_exclusion_mask.xml
diff --git a/registration/9.9.9/notes/registration-strategy.txt b/registration/deprecated/notes/registration-strategy.txt
similarity index 100%
rename from registration/9.9.9/notes/registration-strategy.txt
rename to registration/deprecated/notes/registration-strategy.txt
diff --git a/registration/9.9.9/quality-assessment/compute-registration-quality.R b/registration/deprecated/quality-assessment/compute-registration-quality.R
similarity index 100%
rename from registration/9.9.9/quality-assessment/compute-registration-quality.R
rename to registration/deprecated/quality-assessment/compute-registration-quality.R
diff --git a/registration/9.9.9/quality-assessment/em-fixed-points.txt b/registration/deprecated/quality-assessment/em-fixed-points.txt
similarity index 100%
rename from registration/9.9.9/quality-assessment/em-fixed-points.txt
rename to registration/deprecated/quality-assessment/em-fixed-points.txt
diff --git a/registration/9.9.9/quality-assessment/manually_matched_points.xlsx b/registration/deprecated/quality-assessment/manually_matched_points.xlsx
similarity index 100%
rename from registration/9.9.9/quality-assessment/manually_matched_points.xlsx
rename to registration/deprecated/quality-assessment/manually_matched_points.xlsx
diff --git a/registration/9.9.9/quality-assessment/notes.txt b/registration/deprecated/quality-assessment/notes.txt
similarity index 100%
rename from registration/9.9.9/quality-assessment/notes.txt
rename to registration/deprecated/quality-assessment/notes.txt
diff --git a/registration/9.9.9/quality-assessment/outputpoints.txt b/registration/deprecated/quality-assessment/outputpoints.txt
similarity index 100%
rename from registration/9.9.9/quality-assessment/outputpoints.txt
rename to registration/deprecated/quality-assessment/outputpoints.txt
diff --git a/registration/9.9.9/quality-assessment/transformix.log b/registration/deprecated/quality-assessment/transformix.log
similarity index 100%
rename from registration/9.9.9/quality-assessment/transformix.log
rename to registration/deprecated/quality-assessment/transformix.log
diff --git a/registration/9.9.9/quality-assessment/~$manually_matched_points.xlsx b/registration/deprecated/quality-assessment/~$manually_matched_points.xlsx
similarity index 100%
rename from registration/9.9.9/quality-assessment/~$manually_matched_points.xlsx
rename to registration/deprecated/quality-assessment/~$manually_matched_points.xlsx
diff --git a/registration/9.9.9/scripts/elastix.ijm b/registration/deprecated/scripts/elastix.ijm
similarity index 100%
rename from registration/9.9.9/scripts/elastix.ijm
rename to registration/deprecated/scripts/elastix.ijm
diff --git a/registration/9.9.9/scripts/mask_gut_nuclei.py b/registration/deprecated/scripts/mask_gut_nuclei.py
similarity index 100%
rename from registration/9.9.9/scripts/mask_gut_nuclei.py
rename to registration/deprecated/scripts/mask_gut_nuclei.py
diff --git a/registration/9.9.9/scripts/prepare_image_data.ijm b/registration/deprecated/scripts/prepare_image_data.ijm
similarity index 100%
rename from registration/9.9.9/scripts/prepare_image_data.ijm
rename to registration/deprecated/scripts/prepare_image_data.ijm
diff --git a/registration/9.9.9/scripts/registration_targets/exclude_nuclei_from_table.py b/registration/deprecated/scripts/registration_targets/exclude_nuclei_from_table.py
similarity index 100%
rename from registration/9.9.9/scripts/registration_targets/exclude_nuclei_from_table.py
rename to registration/deprecated/scripts/registration_targets/exclude_nuclei_from_table.py
diff --git a/registration/9.9.9/scripts/registration_targets/move_meds.py b/registration/deprecated/scripts/registration_targets/move_meds.py
similarity index 100%
rename from registration/9.9.9/scripts/registration_targets/move_meds.py
rename to registration/deprecated/scripts/registration_targets/move_meds.py
diff --git a/registration/9.9.9/scripts/registration_targets/set_voxel_size.ijm b/registration/deprecated/scripts/registration_targets/set_voxel_size.ijm
similarity index 100%
rename from registration/9.9.9/scripts/registration_targets/set_voxel_size.ijm
rename to registration/deprecated/scripts/registration_targets/set_voxel_size.ijm
diff --git a/registration/9.9.9/scripts/registration_targets/stomach_registration_targets.py b/registration/deprecated/scripts/registration_targets/stomach_registration_targets.py
similarity index 100%
rename from registration/9.9.9/scripts/registration_targets/stomach_registration_targets.py
rename to registration/deprecated/scripts/registration_targets/stomach_registration_targets.py
diff --git a/registration/9.9.9/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.ijm b/registration/deprecated/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.ijm
similarity index 100%
rename from registration/9.9.9/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.ijm
rename to registration/deprecated/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.ijm
diff --git a/registration/9.9.9/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.sh b/registration/deprecated/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.sh
similarity index 100%
rename from registration/9.9.9/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.sh
rename to registration/deprecated/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.sh
diff --git a/registration/9.9.9/transformations/TransformParameters.BSpline10.9.9.9.txt b/registration/deprecated/transformations/TransformParameters.BSpline10.9.9.9.txt
similarity index 100%
rename from registration/9.9.9/transformations/TransformParameters.BSpline10.9.9.9.txt
rename to registration/deprecated/transformations/TransformParameters.BSpline10.9.9.9.txt
diff --git a/registration/9.9.9/transformations/TransformParameters.BSpline100.9.9.9.txt b/registration/deprecated/transformations/TransformParameters.BSpline100.9.9.9.txt
similarity index 100%
rename from registration/9.9.9/transformations/TransformParameters.BSpline100.9.9.9.txt
rename to registration/deprecated/transformations/TransformParameters.BSpline100.9.9.9.txt
diff --git a/registration/9.9.9/transformations/TransformParameters.BSpline30.9.9.9.txt b/registration/deprecated/transformations/TransformParameters.BSpline30.9.9.9.txt
similarity index 100%
rename from registration/9.9.9/transformations/TransformParameters.BSpline30.9.9.9.txt
rename to registration/deprecated/transformations/TransformParameters.BSpline30.9.9.9.txt
diff --git a/registration/9.9.9/transformations/TransformParameters.RotationPreAlign.0.0.0.txt b/registration/deprecated/transformations/TransformParameters.RotationPreAlign.0.0.0.txt
similarity index 100%
rename from registration/9.9.9/transformations/TransformParameters.RotationPreAlign.0.0.0.txt
rename to registration/deprecated/transformations/TransformParameters.RotationPreAlign.0.0.0.txt
diff --git a/registration/9.9.9/transformations/TransformParameters.Similarity.0.0.0.txt b/registration/deprecated/transformations/TransformParameters.Similarity.0.0.0.txt
similarity index 100%
rename from registration/9.9.9/transformations/TransformParameters.Similarity.0.0.0.txt
rename to registration/deprecated/transformations/TransformParameters.Similarity.0.0.0.txt
diff --git a/registration/9.9.9/transformations/TransformParameters.Similarity.0.txt b/registration/deprecated/transformations/TransformParameters.Similarity.0.txt
similarity index 100%
rename from registration/9.9.9/transformations/TransformParameters.Similarity.0.txt
rename to registration/deprecated/transformations/TransformParameters.Similarity.0.txt
diff --git a/registration/9.9.9/transformations/TransformParameters.Similarity.9.9.9.txt b/registration/deprecated/transformations/TransformParameters.Similarity.9.9.9.txt
similarity index 100%
rename from registration/9.9.9/transformations/TransformParameters.Similarity.9.9.9.txt
rename to registration/deprecated/transformations/TransformParameters.Similarity.9.9.9.txt
--
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