FIX: install + docker https

Dockerfile

@@ -7,7 +7,7 @@ RUN apt-get update && \
     apt-get install -y git build-essential \
       liblapack-dev libopenblas-dev libgl1 libxrender1
 
-RUN git clone git@github.com:scil-vital/TractOracleNet.git
+RUN git clone https://github.com/scil-vital/TractOracleNet.git
 
 WORKDIR /TractOracleNet
 

TractOracleNet/runners/predictor.py

@@ -10,7 +10,7 @@
 from tqdm import tqdm
 
 from scilpy.io.utils import (
-    assert_inputs_exist, assert_outputs_exist)
+    assert_inputs_exist, assert_outputs_exist, add_overwrite_arg)
 
 from TractOracleNet.utils import get_data, save_filtered_streamlines
 from TractOracleNet.models.utils import get_model
@@ -37,7 +37,7 @@ def __init__(
         self.threshold = train_dto['threshold']
         self.batch_size = train_dto['batch_size']
         self.out = train_dto['out']
-        self.save_rejected = train_dto['rejected']
+        self.rejected = train_dto['rejected']
         self.nofilter = train_dto['nofilter']
 
     def predict(self, model, sft):
@@ -133,22 +133,25 @@ def run(self):
             predictions = self.predict(model, sft)
 
         # Save the filtered streamlines
-        if not self.nofilter and not self.dense:
+        if not self.dense:
             # Fetch the streamlines that passed the gauntlet
-            ids = np.argwhere(
-                predictions > self.threshold).squeeze()
+            if self.nofilter:
+                ids = np.arange(0, len(predictions))
+            else:
+                # Save the filtered streamlines
+                print('Kept {}/{} streamlines ({}%).'.format(len(ids),
+                      len(sft), (len(ids) / len(sft) * 100)))
 
-            new_sft = StatefulTractogram.from_sft(sft[ids].streamlines, sft)
+                ids = np.argwhere(
+                    predictions > self.threshold).squeeze()
 
-            # Save the filtered streamlines
-            print('Kept {}/{} streamlines ({}%).'.format(len(ids),
-                  len(sft), (len(ids) / len(sft) * 100)))
+            new_sft = StatefulTractogram.from_sft(sft[ids].streamlines, sft)
 
             # Save the streamlines
             save_filtered_streamlines(new_sft, predictions[ids], self.out)
 
             # Save the streamlines that rejected
-            if self.save_rejected:
+            if self.rejected:
                 # Fetch the streamlines that rejected
                 rejected_ids = np.setdiff1d(np.arange(predictions.shape[0]),
                                             ids)
@@ -158,7 +161,7 @@ def run(self):
 
                 # Save the streamlines
                 save_filtered_streamlines(
-                    new_sft, predictions[rejected_ids], self.save_rejected)
+                    new_sft, predictions[rejected_ids], self.rejected)
         else:
             # Save all streamlines
             sft.data_per_point['score'] = predictions
@@ -199,6 +202,7 @@ def _build_arg_parser(parser):
                         ' Streamlines\' endpoints should be uniformized for'
                         ' best visualization.')
 
+    add_overwrite_arg(parser)
 
 def parse_args():
     """ Filter a tractogram. """

install.sh

@@ -13,12 +13,8 @@ if [ -x "$(command -v nvidia-smi)" ]; then
     FOUND_CUDA=$(nvidia-smi | grep "CUDA Version" | awk '{print $9}' | sed 's/\.//g')
     if (( $FOUND_CUDA == 116 )); then
         CUDA_VERSION="cu116"
-    elif (( $FOUND_CUDA == 117 )); then
+    elif (( $FOUND_CUDA >= 117 )); then
         CUDA_VERSION="cu117"
-    elif (( $FOUND_CUDA == 118 )); then
-        CUDA_VERSION="cu118"
-    elif (( $FOUND_CUDA == 121 )); then
-        CUDA_VERSION="cu121"
     else
       CUDA_VERSION="cpu"
       echo "CUDA version ${FOUND_CUDA} is not compatible. Installing PyTorch without CUDA support."