block transferToServer if a crop is happening

Author: raacampbell

.gitignore

@@ -1,2 +1,4 @@
 *.pyc
-
+btpytools.egg-info/
+build/
+dist/

.idea/misc.xml

@@ -17,6 +17,7 @@
 DOWNSAMPLED_STACK_SUB_DIR = "*_micron"  # Sub-directories in DOWNSAMPLED_DIR
 DOWNSAMPLED_STACK_LOG_FILE = "ds_*.txt"  # Wildcard for downsampled stacks
 UNCROPPED_WILDCARD = "./Uncropped*_DELETE_ME_DELETE_ME"
+CROPPED_TEMP_DIR_WILDCARD = "CROP_stitchedImages_*"
 RECIPE_WILDCARD = "recipe*.yml"
 
 # Related to registration directories.
@@ -105,6 +106,15 @@ def has_uncropped_stitched_images(t_path=""):
     return file_glob_exist(t_path)
 
 
+def is_currently_cropping(t_path=""):
+    """Check if cropping is currently happening by looking for the temp dir
+    that the stitchit.sampleSplitter created.
+    Returns True if cropping right now, False otherwise.
+    """
+    t_path = os.path.join(t_path, CROPPED_TEMP_DIR_WILDCARD)
+    return file_glob_exist(t_path)
+
+
 def is_data_folder(dirToTest="", verbose=False):
     """is directory "dirToTest" a BakingTray data directory?
     i.e. it satisfies the following criteria:

btpytools.egg-info/.gitignore

@@ -425,8 +425,15 @@ def main():
     if check_directories(source_dirs, destination_dir):
         sys.exit()
 
+    # Bail out if we find any folders at all that have not finished cropping
+    for t_dir in source_dirs:
+        if tools.is_currently_cropping(t_dir):
+            print("Directory '%s' is currently being cropped. QUITTING." % t_dir)
+            sys.exit()
+
     # Remove trailing slash from data directories that don't contain data sub-directories
     for _ii, t_dir in enumerate(source_dirs):
+
         if tools.is_data_folder(t_dir) and not tools.contains_data_folders(t_dir):
             # If here, tDIR is a sample folder without sub-folders. If there is a
             # trailing slash then we should delete it. Always.

btpytools/tools.py

@@ -0,0 +1,10 @@
+main: {borderPixSize: 4.0, medFiltRawImage: 5.0, doTiledMerge: true, tiledMergeThresh: 1.05,
+  defaultThreshSD: 7.0, reCalcThreshSD_threshold: 10.0, rescaleTo: 50.0}
+mainBin: {removeNoise: true, medFiltBW: 5.0, primaryShape: disk, primaryFiltSize: 50.0,
+  expansionShape: square, doExpansion: true, expansionSize: 600.0}
+mainGetBB: {minSizeInSqMicrons: 15000.0}
+clipper: {doExtension: true, edgeThreshMicrons: 350.0, growROIbyMicrons: 450.0}
+mergeO: {mergeThresh: 1.3}
+stackStr: {rollingThreshold: true, nImages: 5.0}
+autoThresh: {skipMergeNROIThresh: 10.0, doBinaryExpansion: false, minThreshold: 2.0,
+  maxThreshold: 12.0, allowMaxExtensionIfFewThreshLeft: true, decreaseThresholdBy: 0.9}