vqdang · vqdang · Jan 29, 2021 · Mar 2, 2021 · Mar 2, 2021 · Mar 3, 2021
diff --git a/.gitignore b/.gitignore
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -12,6 +12,21 @@
             "program": "${file}",
             "console": "integratedTerminal",
             "cwd" : "${fileDirname}", // run at the location of the runfile
+            // hook terminal cmd to debug file
+            "args": [
+                // "--gpu=0",
+                "--nr_types=6",
+                "--type_info_path=type_info.json",
+                "--batch_size=64",
+                "--model_mode=fast",
+                "--model_path=../../pretrained/hovernet_fast_pannuke_pytorch.tar",
+                "--nr_inference_workers=4",
+                "--nr_post_proc_workers=8",
+                "wsi",
+                "--ambiguous_size=328",
+                "--input_dir=exp_output/wsi/samples/",
+                "--output_dir=exp_output/wsi/pred/",
+            ]
         },
         {
             "name": "Python: Remote Attach",

diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
diff --git a/__init__.py b/__init__.py
diff --git a/compute_stats.py b/compute_stats.py
diff --git a/config.py b/config.py
diff --git a/convert_chkpt_tf2pytorch.py b/convert_chkpt_tf2pytorch.py
diff --git a/convert_format.py b/convert_format.py
@@ -55,7 +55,7 @@ def rgb2int(rgb):
     target_format = "qupath"
     # to rescale the coordinate set to match with lv0 mag of the wsi
     scale_factor = 1.0
-    root_dir = "dataset/dummy/out/"
+    root_dir = "exp_output/wsi/pred/"
 
     # to define the name, and color conversion code for each target format
     type_info_dict = {

diff --git a/dataloader/__init__.py b/dataloader/__init__.py
diff --git a/dataloader/augs.py b/dataloader/augs.py
diff --git a/dataloader/infer_loader.py b/dataloader/infer_loader.py
diff --git a/dataloader/train_loader.py b/dataloader/train_loader.py
diff --git a/dataset.py b/dataset.py
diff --git a/diagram.png b/diagram.png
diff --git a/docs/diagram.png b/docs/diagram.png
diff --git a/docs/seg.gif b/docs/seg.gif
diff --git a/environment.yml b/environment.yml
diff --git a/examples/.ipynb_checkpoints/usage-checkpoint.ipynb b/examples/.ipynb_checkpoints/usage-checkpoint.ipynb
diff --git a/examples/usage.ipynb b/examples/usage.ipynb
diff --git a/extract_patches.py b/extract_patches.py
diff --git a/infer/__init__.py b/infer/__init__.py
diff --git a/infer/base.py b/infer/base.py
@@ -67,11 +67,11 @@ def __load_model(self):
 
         net.load_state_dict(saved_state_dict, strict=True)
         net = torch.nn.DataParallel(net)
-        net = net.to("cuda")
+        self.model = net.to("cuda")
 
         module_lib = import_module("models.hovernet.run_desc")
-        run_step = getattr(module_lib, "infer_step")
-        self.run_step = lambda input_batch: run_step(input_batch, net)
+        self.run_step = getattr(module_lib, "infer_step")
+        # self.run_step = lambda input_batch: run_step(input_batch, net)       
 
         module_lib = import_module("models.hovernet.post_proc")
         self.post_proc_func = getattr(module_lib, "process")