corrected prediction module

Author: Soorya19Pradeep

examples/infection_phenotyping/test_infection_classifier.py

@@ -6,7 +6,7 @@
 from viscy.data.hcs import Sample
 import lightning.pytorch as pl
 import torch
-
+import torchmetrics
 from viscy.light.predict_writer import HCSPredictionWriter
 from monai.transforms import DivisiblePad
 
@@ -16,7 +16,7 @@
 data_module = HCSDataModule(
     test_datapath,
     source_channel=["Sensor", "Phase"],
-    target_channel=[],
+    target_channel=["inf_mask"],
     split_ratio=0.8,
     z_window_size=1,
     architecture="2D",
@@ -36,8 +36,6 @@
 data_module.prepare_data()
 
 data_module.setup(stage="predict")
-test_dm = data_module.test_dataloader()
-sample = next(iter(test_dm))
 
 # %%
 class LightningUNet(pl.LightningModule):
@@ -49,6 +47,9 @@ def __init__(
     ):
         super(LightningUNet, self).__init__()
         self.unet_model = Unet2d(in_channels=in_channels, out_channels=out_channels)
+        # self.pred_cm = torchmetrics.classification.ConfusionMatrix(  
+        #     task="multiclass", num_classes=self.n_classes  
+        # ) 
         if ckpt_path is not None:
             state_dict = torch.load(ckpt_path, map_location=torch.device("cpu"))[
                 "state_dict"
@@ -62,8 +63,8 @@ def forward(self, x):
     def predict_step(self, batch: Sample, batch_idx: int, dataloader_idx: int = 0):
         source = self._predict_pad(batch["source"])
         pred_class = self.forward(source)
-        pred_int = torch.argmax(pred_class, dim=4, keepdim=True)
-        return self._predict_pad.inverse(pred_int)
+        pred_int = torch.argmax(pred_class, dim=1, keepdim=True)
+        return pred_int
 
     def on_predict_start(self):
         """Pad the input shape to be divisible by the downsampling factor.
@@ -79,7 +80,7 @@ def on_predict_start(self):
 
 trainer = pl.Trainer(
     default_root_dir="/hpc/projects/intracellular_dashboard/viral-sensor/infection_classification/models/sensorInf_phenotyping/logs_wPhase",
-    callbacks=[HCSPredictionWriter(output_path, write_input=True)],
+    callbacks=[HCSPredictionWriter(output_path, write_input=False)],
 )
 model = LightningUNet(
     in_channels=2,