Update BatchProcessing

DeepLabCut · n-poulsen · Feb 10, 2025 · Feb 5, 2025 · Feb 7, 2025 · Jan 29, 2025
commit c890473081f32f5d9829e10ca31b2fa9074570eb
diff --git a/docs/recipes/BatchProcessing.md b/docs/recipes/BatchProcessing.md
@@ -3,10 +3,12 @@
 
 ## Tips for working with DLC networks:
 
-- Now you have a DLC network and are happy with the performance on selected videos, you may want to run it on all your videos without hassle. If all your videos are in one folder this is easy, simply pass the foldername to `deeplabcut.analyze_videos(config,[folder])` and you are fine. What if the videos are scattered?
+Now you have a DLC network and are happy with the performance on selected videos, you may want to run it on all your
+videos without hassle. If all your videos are in one folder this is easy, simply pass the foldername to
+`deeplabcut.analyze_videos(config,[folder])` and you are fine. What if the videos are scattered?
 
-
-You could create a simply script that runs over all your video folders with the network of choice. Your "key" to this network is your config.yaml file.
+You can create a simple script that runs over all your video folders with the network of choice. Your "key" to this
+network is your config.yaml file.
 
 ![](https://static1.squarespace.com/static/57f6d51c9f74566f55ecf271/t/5ccc5abe0d9297405a428522/1556896461304/howtouseDLC-01.png?format=1000w)
 
@@ -33,18 +35,18 @@ import deeplabcut
 
 def getsubfolders(folder):
     ''' returns list of subfolders '''
-    return [os.path.join(folder,p) for p in os.listdir(folder) if os.path.isdir(os.path.join(folder,p))]
+    return [os.path.join(folder, p) for p in os.listdir(folder) if os.path.isdir(os.path.join(folder, p))]
 
-project='ComplexWheelD3-12-Fumi-2019-01-28'
+project = "ComplexWheelD3-12-Fumi-2019-01-28"
 
-shuffle=1
+shuffle = 1
 
-prefix='/home/alex/DLC-workshopRowland'
+prefix = "/home/alex/DLC-workshopRowland"
 
-projectpath=os.path.join(prefix,project)
-config=os.path.join(projectpath,'config.yaml')
+projectpath = os.path.join(prefix, project)
+config = os.path.join(projectpath, "config.yaml")
 
-basepath='/home/alex/BenchmarkingExperimentsJan2019' #data'
+basepath = "/home/alex/BenchmarkingExperimentsJan2019"
 
 '''
 
@@ -57,13 +59,13 @@ Imagine that the data (here: videos of 3 different types) are in subfolders:
 
 '''
 
-subfolders=getsubfolders(basepath)
+subfolders = getsubfolders(basepath)
 for subfolder in subfolders: #this would be January, February etc. in the upper example
-    print("Starting analyze data in:", subfolder)
-    subsubfolders=getsubfolders(subfolder)
+    print("Starting analyze data in: ", subfolder)
+    subsubfolders = getsubfolders(subfolder)
     for subsubfolder in subsubfolders: #this would be Febuary1, etc. in the upper example...
-        print("Starting analyze data in:", subsubfolder)
-        for vtype in ['.mp4','.m4v','.mpg']:
+        print("Starting analyze data in: ", subsubfolder)
+        for vtype in [".mp4", ".m4v", ".mpg"]:
             deeplabcut.analyze_videos(config,[subsubfolder],shuffle=shuffle,videotype=vtype,save_as_csv=True)
 
 ```
@@ -90,48 +92,44 @@ import os
 
 import deeplabcut
 
-Maxiter=int(1.5*10**5)
+epochs = 200
 
 model=int(sys.argv[1])
 
-Projects=[['project1-phoenix-2019-01-28'],['ComplexWheelD3-12-Fumi-2019-01-28', 'maze-ariel-2019-01-28'], ['TBI-BvA-2019-01-28','group-eli-2019-01-28']]
+Projects=[["project1-phoenix-2019-01-28"], ["ComplexWheelD3-12-Fumi-2019-01-28", "maze-ariel-2019-01-28"], ["TBI-BvA-2019-01-28", "group-eli-2019-01-28"]]
 
 shuffle=1
 
-prefix='/home/alex/DLC-workshopRowland'
+prefix = "/home/alex/DLC-workshopRowland"
 
 for project in Projects[model]:
-    projectpath=os.path.join(prefix,project)
-    config=os.path.join(projectpath,'config.yaml')
+    projectpath = os.path.join(prefix, project)
+    config = os.path.join(projectpath, "config.yaml")
 
-    cfg=deeplabcut.auxiliaryfunctions.read_config(config)
-    previous_path=cfg['project_path']
+    cfg = deeplabcut.auxiliaryfunctions.read_config(config)
+    previous_path = cfg["project_path"]
 
-    cfg['project_path']=projectpath
-    deeplabcut.auxiliaryfunctions.write_config(config,cfg)
+    cfg["project_path"]=projectpath
+    deeplabcut.auxiliaryfunctions.write_config(config, cfg)
 
     print("This is the name of the script: ", sys.argv[0])
     print("Shuffle: ", shuffle)
     print("config: ", config)
 
     deeplabcut.create_training_dataset(config, Shuffles=[shuffle])
 
-    deeplabcut.train_network(config, shuffle=shuffle, max_snapshots_to_keep=5, maxiters=Maxiter)
+    deeplabcut.train_network(config, shuffle=shuffle, max_snapshots_to_keep=5, epochs=epochs)
     print("Evaluating...")
-    deeplabcut.evaluate_network(config, Shuffles=[shuffle],plotting=True)
+    deeplabcut.evaluate_network(config, Shuffles=[shuffle], plotting=True)
 
     print("Analyzing videos..., switching to last snapshot...")
-    #cfg=deeplabcut.auxiliaryfunctions.read_config(config)
-    #cfg['snapshotindex']=-1
-    #deeplabcut.auxiliaryfunctions.write_config(config,cfg)
-
     for vtype in ['.mp4','.m4v','.mpg']:
         try:
-            deeplabcut.analyze_videos(config,[str(os.path.join(projectpath,'videos'))],shuffle=shuffle,videotype=vtype,save_as_csv=True)
+            deeplabcut.analyze_videos(config, [str(os.path.join(projectpath, "videos"))], shuffle=shuffle, videotype=vtype, save_as_csv=True)
         except:
             pass
 
     print("DONE WITH ", project," resetting to original path")
-    cfg['project_path']=previous_path
-    deeplabcut.auxiliaryfunctions.write_config(config,cfg)
+    cfg["project_path"] = previous_path
+    deeplabcut.auxiliaryfunctions.write_config(config, cfg)
     ```