fix(scripts): keep folder structure of input for processed folder

MedVisBonn · Jan 31, 2022 · bb6bcef · bb6bcef
1 parent c76b306
commit bb6bcef
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Showing 7 changed files with 173 additions and 149 deletions.
diff --git a/octseg/scripts/commands/drusen.py b/octseg/scripts/commands/drusen.py
@@ -61,7 +61,8 @@ def drusen(ctx: click.Context, drusen_threshold, overwrite):
             # Load data
             data = data_readers[datatype](path)
             # Read layers
-            layers_filepath = output_path / path.stem / "layers.pkl"
+            output_dir = output_path / path.relative_to(input_path).parent / path.stem
+            layers_filepath = output_dir / "layers.pkl"
             try:
                 with open(layers_filepath, "rb") as myfile:
                     layers = pickle.load(myfile)
@@ -78,7 +79,8 @@ def drusen(ctx: click.Context, drusen_threshold, overwrite):
             # Compute drusen
             drusen = drusen2d(data.layers["RPE"], data.layers["BM"], data.shape)
             clean_drusen = filter_by_height(drusen, minimum_height=drusen_threshold)
-            drusen_filepath = output_path / path.stem / "drusen.pkl"
+            output_dir = output_path / path.relative_to(input_path).parent / path.stem
+            drusen_filepath = output_dir / "drusen.pkl"
             with open(drusen_filepath, "wb") as myfile:
                 pickle.dump(clean_drusen, myfile)
 

diff --git a/octseg/scripts/commands/layers.py b/octseg/scripts/commands/layers.py
@@ -85,7 +85,7 @@ def layers(ctx: click.Context, model_id, overwrite, gpu):
             # Predict layers
             data = get_layers(data, model_id)
             # Save predicted layers
-            output_dir = output_path / path.stem
+            output_dir = output_path / path.relative_to(input_path).parent / path.stem
             output_dir.mkdir(parents=True, exist_ok=True)
             with open(output_dir / ("layers.pkl"), "wb") as myfile:
                 pickle.dump(data.layers, myfile)

diff --git a/octseg/scripts/commands/plot_bscans.py b/octseg/scripts/commands/plot_bscans.py
@@ -66,8 +66,9 @@ def plot_bscans(ctx: click.Context, drusen, layers, volumes):
             # Load data
             data = data_readers[datatype](path)
             # Load layers and drusen
-            layers_filepath = output_path / path.stem / "layers.pkl"
-            drusen_filepath = output_path / path.stem / "drusen.pkl"
+            output_dir = output_path / path.relative_to(input_path).parent / path.stem
+            layers_filepath = output_dir / "layers.pkl"
+            drusen_filepath = output_dir / "drusen.pkl"
 
             try:
                 with open(layers_filepath, "rb") as myfile:
@@ -89,7 +90,13 @@ def plot_bscans(ctx: click.Context, drusen, layers, volumes):
                     bscan.layers[key] = heights
             data._drusen = drusen_data
 
-            save_path = output_path / "plots" / "bscans" / path.stem
+            save_path = (
+                output_path
+                / "plots"
+                / "bscans"
+                / path.relative_to(input_path).parent
+                / path.stem
+            )
             save_path.mkdir(parents=True, exist_ok=True)
             for bscan in tqdm(data):
                 bscan.plot(drusen=drusen, layers=layers)

diff --git a/octseg/scripts/commands/plot_enface.py b/octseg/scripts/commands/plot_enface.py
@@ -46,8 +46,9 @@ def plot_enface(ctx: click.Context, drusen, bscan_area, bscan_positions):
             # Load data
             data = data_readers[datatype](path)
             # Load layers and drusen
-            layers_filepath = output_path / path.stem / "layers.pkl"
-            drusen_filepath = output_path / path.stem / "drusen.pkl"
+            output_dir = output_path / path.relative_to(input_path).parent / path.stem
+            layers_filepath = output_dir / "layers.pkl"
+            drusen_filepath = output_dir / "drusen.pkl"
 
             try:
                 with open(layers_filepath, "rb") as myfile:
@@ -69,7 +70,13 @@ def plot_enface(ctx: click.Context, drusen, bscan_area, bscan_positions):
                     bscan.layers[key] = heights
             data._drusen = drusen_data
 
-            save_path = output_path / "plots" / "enface"
+            save_path = (
+                output_path
+                / "plots"
+                / "enface"
+                / path.relative_to(input_path).parent
+                / path.stem
+            )
             save_path.mkdir(parents=True, exist_ok=True)
 
             if not bscan_positions:

diff --git a/octseg/scripts/commands/quantify.py b/octseg/scripts/commands/quantify.py
@@ -64,8 +64,9 @@ def quantify(ctx: click.Context, radii, sectors, offsets):
             # Load data
             data = data_readers[datatype](path)
             # Read layers
-            layers_filepath = output_path / path.stem / "layers.pkl"
-            drusen_filepath = output_path / path.stem / "drusen.pkl"
+            output_dir = output_path / path.relative_to(input_path).parent / path.stem
+            layers_filepath = output_dir / "layers.pkl"
+            drusen_filepath = output_dir / "drusen.pkl"
 
             try:
                 with open(layers_filepath, "rb") as myfile: