bugs

MWTracker/trackWorms/getWormTrajectories.py

@@ -626,7 +626,7 @@ def joinTrajectories(trajectories_file, min_track_size = 50, \
 
         #read the worm_index column, this is the index order that have to be conserved in the worm_index_joined column
         worm_index = plate_worms.col('worm_index')
-        _worm_index_joined = joinDict2Index(worm_index, relations_dict, valid_indexes)
+        worm_index_joined = _joinDict2Index(worm_index, relations_dict, valid_indexes)
 
         #add the result the column worm_index_joined
         plate_worms.modify_column(colname = 'worm_index_joined', column = worm_index_joined)

Tests/run_tests.sh

@@ -0,0 +1,39 @@
+EXAMPLES_DIR="/Users/ajaver/Google Drive/MWTracker_Example"
+SCRIPT_DIR=/Users/ajaver/Documents/GitHub/Multiworm_Tracking/cmd_scripts
+
+TEST1_DIR="$EXAMPLES_DIR/test_1"
+TEST2_DIR="$EXAMPLES_DIR/test_2"
+TEST3_DIR="$EXAMPLES_DIR/test_3"
+
+
+function test1 {
+echo "%%%% TEST1 %%%%"
+chflags -R nouchg "$TEST1_DIR/MaskedVideos"
+rm -Rf "$TEST1_DIR/MaskedVideos"
+python3  "$SCRIPT_DIR/compressMultipleFiles.py" "$TEST1_DIR/RawVideos" "$TEST1_DIR/MaskedVideos"
+}
+
+function test2 {
+echo "%%%% TEST2 %%%%"
+chflags -R nouchg "$TEST2_DIR/MaskedVideos"
+rm -Rf "$TEST2_DIR/MaskedVideos"
+
+python3  "$SCRIPT_DIR/compressMultipleFiles.py" "$TEST2_DIR/RawVideos" "$TEST2_DIR/MaskedVideos" \
+--json_file "$TEST2_DIR/test2.json" --pattern_include "*.avi"
+}
+
+function test3 {
+echo "%%%% TEST3 %%%%"
+rm -Rf "$TEST3_DIR/Results"
+python3  "$SCRIPT_DIR/trackMultipleFiles.py" "$TEST3_DIR/MaskedVideos" --json_file "$TEST3_DIR/test3.json"
+}
+
+function clean_all {
+rm -Rf "$TEST1_DIR/MaskedVideos"
+rm -Rf "$TEST2_DIR/MaskedVideos"
+rm -Rf "$TEST3_DIR/Results"
+}
+
+#test1
+#test1
+test3

single_worm_db/compress_mac1.sh

@@ -1,12 +1,12 @@
 python3 ~/Documents/GitHub/Multiworm_Tracking/cmd_scripts/compressMultipleFiles.py \
 /Volumes/behavgenom_archive\$/thecus /Volumes/behavgenom_archive\$/MaskedVideos \
---json_file ~/Documents/GitHub/Multiworm_Tracking/JSON_singleworm/swimming.json \
+--json_file ~/Documents/GitHub/Multiworm_Tracking/single_worm_db/JSON_singleworm/swimming.json \
 --is_copy_video --is_single_worm --max_num_process 21 \
 --videos_list ~/Documents/GitHub/Multiworm_Tracking/single_worm_db/videos_swimming_1
 
 python3 ~/Documents/GitHub/Multiworm_Tracking/cmd_scripts/compressMultipleFiles.py \
  /Volumes/behavgenom_archive\$/thecus /Volumes/behavgenom_archive\$/MaskedVideos \
- --json_file ~/Documents/GitHub/Multiworm_Tracking/JSON_singleworm/on_food.json \
+ --json_file ~/Documents/GitHub/Multiworm_Tracking/single_worm_db/JSON_singleworm/on_food.json \
  --is_copy_video --is_single_worm --max_num_process 21 \
  --videos_list ~/Documents/GitHub/Multiworm_Tracking/single_worm_db/videos_agar_1
 

single_worm_db/compress_mac2.sh

@@ -1,12 +1,12 @@
 python3 ~/Documents/GitHub/Multiworm_Tracking/cmd_scripts/compressMultipleFiles.py \
 /Volumes/behavgenom_archive\$/thecus /Volumes/behavgenom_archive\$/MaskedVideos \
---json_file ~/Documents/GitHub/Multiworm_Tracking/JSON_singleworm/swimming.json \
+--json_file ~/Documents/GitHub/Multiworm_Tracking/single_worm_db/JSON_singleworm/swimming.json \
 --is_copy_video --is_single_worm --max_num_process 24 \
 --videos_list ~/Documents/GitHub/Multiworm_Tracking/single_worm_db/videos_swimming_2
 
 python3 ~/Documents/GitHub/Multiworm_Tracking/cmd_scripts/compressMultipleFiles.py \
  /Volumes/behavgenom_archive\$/thecus /Volumes/behavgenom_archive\$/MaskedVideos \
- --json_file ~/Documents/GitHub/Multiworm_Tracking/JSON_singleworm/on_food.json \
+ --json_file ~/Documents/GitHub/Multiworm_Tracking/single_worm_db/JSON_singleworm/on_food.json \
  --is_copy_video --is_single_worm --max_num_process 24 \
  --videos_list ~/Documents/GitHub/Multiworm_Tracking/single_worm_db/videos_agar_2
 

single_worm_db/track_mac1.sh

@@ -1,12 +1,12 @@
 python3 ~/Documents/GitHub/Multiworm_Tracking/cmd_scripts/trackMultipleFiles.py \
 /Volumes/behavgenom_archive\$/MaskedVideos \
---json_file ~/Documents/GitHub/Multiworm_Tracking/JSON_singleworm/swimming.json \
+--json_file ~/Documents/GitHub/Multiworm_Tracking/single_worm_db/JSON_singleworm/swimming.json \
 --is_single_worm --max_num_process 21 --end_point INT_SKE_ORIENT \
 --videos_list ~/Documents/GitHub/Multiworm_Tracking/single_worm_db/masks_swimming_1
 
 python3 ~/Documents/GitHub/Multiworm_Tracking/cmd_scripts/trackMultipleFiles.py \
 /Volumes/behavgenom_archive\$/MaskedVideos \
---json_file ~/Documents/GitHub/Multiworm_Tracking/JSON_singleworm/on_food.json \
+--json_file ~/Documents/GitHub/Multiworm_Tracking/single_worm_db/JSON_singleworm/on_food.json \
 --is_single_worm --max_num_process 21 --end_point INT_SKE_ORIENT \
 --videos_list ~/Documents/GitHub/Multiworm_Tracking/single_worm_db/masks_agar_1
 

single_worm_db/track_mac2.sh

@@ -1,12 +1,12 @@
 python3 ~/Documents/GitHub/Multiworm_Tracking/cmd_scripts/trackMultipleFiles.py \
 /Volumes/behavgenom_archive\$/MaskedVideos \
---json_file ~/Documents/GitHub/Multiworm_Tracking/JSON_singleworm/swimming.json \
+--json_file ~/Documents/GitHub/Multiworm_Tracking/single_worm_db/JSON_singleworm/swimming.json \
 --is_single_worm --max_num_process 21 --end_point INT_SKE_ORIENT \
 --videos_list ~/Documents/GitHub/Multiworm_Tracking/single_worm_db/masks_swimming_2
 
 python3 ~/Documents/GitHub/Multiworm_Tracking/cmd_scripts/trackMultipleFiles.py \
 /Volumes/behavgenom_archive\$/MaskedVideos \
---json_file ~/Documents/GitHub/Multiworm_Tracking/JSON_singleworm/on_food.json \
+--json_file ~/Documents/GitHub/Multiworm_Tracking/single_worm_db/JSON_singleworm/on_food.json \
 --is_single_worm --max_num_process 21 --end_point INT_SKE_ORIENT \
 --videos_list ~/Documents/GitHub/Multiworm_Tracking/single_worm_db/masks_agar_2