example script updated to automatically handle multiple models (e.g. …

…HBP-2022Q2/)

examples/simple_transfer.py

@@ -1,31 +1,81 @@
 
-import shutil, os, sys
+import shutil, os, sys, argparse
 sys.path.append('../tools')
 
 from transfer import SimpleTransfer as strans
 
 '''
-if mechnisms.json, 
-   parameters.json and 
-   best_models.json 
-all in base of source 
-and morphology is in
-    source/morphology 
-specifying source and destination is all that should be needed
-'''
+run this file with arguments or change the paths to source and destination
+below (source and new_celltype_path, respectively)
+
+    $ python simple_transfer.py -s <source> -d <destination>
+
+In order to use hall_of_fame instead of best_models (default)  
+use the -h argument and send the path to the file
+
+    $ python simple_transfer.py -hof path/hall_off_fame.json
 
-# Please specify/update these paths, below
-# ---------------------------------------------------------------
-source_path         = '../examples/example-option-2' # extra path added for illustration
-new_celltype_path   = '../data/neurons/striatum/test'
-# ---------------------------------------------------------------
+use the -rm/--delete argument to delete the destination folder before transfer (if exists)
+    
+    $ python simple_transfer.py -rm 1
 
+TODO: 
+-verify transfer
+'''
+
+parser = argparse.ArgumentParser(description='Simple program for transfer (conversion) of BPO models into snudda')
+parser.add_argument('-s','--sours', help='source directory')
+parser.add_argument('-a','--all', help='transfer all models in directory (sub directories)', default=0)
+parser.add_argument('-d','--destination', help='destination argument')
+parser.add_argument('-hof','--hall_off_fame', help='list of best models (best_models/hall_off_fame)', default=None)
+parser.add_argument('-rm','--delete', help='delete destination', default=0)
+args = vars(parser.parse_args())    
 
-# create new folder for storing the new cell (using the same name as the source)
-source_name = os.path.split(source_path)[-1]
-new_cell_path = '{}/{}'.format(new_celltype_path, source_name) # past the name of the source model to the celltype path
-os.makedirs(new_cell_path, exist_ok=True)
+def do_transfer(source_path, new_cell_path, hof):
+    print('\n--------------------')
+    print(f'tranfering source: \n\t{source_path} \nto destination \n\t{new_cell_path}\n')
+    strans.SimpleTransfer(source_path, new_cell_path, optimisation_result_file=hof)
 
+# Please specify/update these paths, below (if not added as argument(s))
+# -------------------------------------------------------------------
+if args['sours']:
+    source_path = args['sours'].strip('/')
+else:
+    # update here
+    source_path = '../examples/example-option-2' # extra path added for illustration
+
+if args['destination']:
+    new_celltype_path = args['destination']
+else:
+    # update here
+    new_celltype_path = '../data/neurons/striatum/test'
+# -------------------------------------------------------------------
 
 # do the transfer
-strans.SimpleTransfer(source_path, new_cell_path)
+if args['all']:
+    subdir = [ f.name for f in os.scandir(source_path) if f.is_dir() ]
+    print(subdir)
+    for d in subdir:
+        celltype = d.split('-')[1] # this is hardcoded and assumes that the type is in the first location of the filename
+        destination = os.path.join(new_celltype_path, celltype, d)
+        sub_source_path = os.path.join(source_path, d)
+        if int(args['delete']) and os.path.isdir(destination):
+            shutil.rmtree(destination)
+        os.makedirs(destination, exist_ok=True)
+        do_transfer(sub_source_path, destination, args['hall_off_fame'])
+else:
+    if int(args['delete']):
+        shutil.rmtree(new_celltype_path)
+
+    # create a new folder for storing the new cell (using the same name as the source)
+    if os.path.normpath(source_path).count(os.sep): # this check if there are more than one level in the path
+        source_name = os.path.split(source_path)[-1]
+    else:
+        source_name = source_path
+
+    new_cell_path = '{}/{}'.format(new_celltype_path, source_name) # past the name of the source model to the celltype path
+    os.makedirs(new_cell_path, exist_ok=True)
+
+    do_transfer(source_path, new_cell_path, args['hall_off_fame'])
+
+

tools/transfer/SimpleTransfer.py

@@ -10,11 +10,12 @@ class SimpleTransfer:
     """
     Class to Transfer all the files from Bluepyopt format to Snudda
     
-    By default assumes that the files listed below are all in the base of source
-        if not, one can specify each path directly by passing them as arguments
+    By default assumes that the files
         -mechanisms.json
         -parameters.json
+    are located in the config folder of the source, and that 
         -best_model.json 
+    are in the base of source
     
     if you are using hall_of_fame.json instead of best_models.json,
         please set the optimization_result_file directly
@@ -38,29 +39,31 @@ def __init__(self,  source,
         self.destination = destination
 
         if not optimisation_result_file:
-            self.optimisation_result_file = '{}/best_models.json'.format(source)
+            self.optimisation_result_file = f'{source}/best_models.json'
         else:
             self.optimisation_result_file = optimisation_result_file
 
         if not mechanisms_path_folder:
-            self.mechanisms_path_folder = source
+            self.mechanisms_path_folder = f'{source}/config'
         else:
             self.mechanisms_path_folder = mechanisms_path_folder
 
         if not parameters_path_folder:
-            self.parameters_path_folder = '{}/parameters.json'.format(source)
+            self.parameters_path_folder = f'{source}/config/parameters.json'
         else:
             self.parameters_path_folder = parameters_path_folder
 
         if not morphology_path_folder:
-            self.morphology_path_folder = '{}/morphology'.format(source)
+            self.morphology_path_folder = f'{source}/morphology'
         else:
             self.morphology_path_folder = morphology_path_folder
 
         self.selected = selected
         self.selected_models = selected_models
 
         self.transfer()
+
+        print('\n---transfer complete---')
 
     def transfer(self):
 

tools/transfer/mechanisms.py

@@ -21,3 +21,5 @@ def transfer_mechanisms(source=None, destination=None, direct_path=None):
     if not os.path.exists(destination):
         os.mkdir(destination)
     shutil.copy(mechanisms_path, os.path.join(destination, "mechanisms.json"))
+
+    print("mechanims file transfer complete")

tools/transfer/morphology.py

@@ -27,6 +27,7 @@ def transfer_morphologies(source=None, destination=None, selected=False, direct_
 
     if direct_path_morph:
         morphology_directory = os.path.join(direct_path_morph)
+        source = os.path.split(direct_path_morph)[0]
     else:
         morphology_directory = os.path.join(source, "morphology")
 
@@ -64,9 +65,6 @@ def transfer_morphologies(source=None, destination=None, selected=False, direct_
         with open(os.path.join(morphology_destination, "morphology_hash_filename.json"), "w") as f:
             json.dump(hash_name_dict, f, indent=4, sort_keys=True)
 
-        print(f"Morphology file transfer complete \n"
-              f" \n"
-              f"from : {source} \n"
-              f"to : {destination} \n")
+        print("Morphology file transfer complete")
 
 

tools/transfer/parameters.py

@@ -188,3 +188,4 @@ def transfer_parameters(source=None, destination=None, direct_path_param=None,
                                                       parameters_path=parameters_path,
                                                       best_models_path=best_models_path,
                                                       selected=selected)
+    print("Parameter file transfer complete")