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Fixes for end-to-end notebooks #5

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10 changes: 6 additions & 4 deletions MONAICore/3. End-To-End Workflow with MONAI - Solution.ipynb
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Expand Up @@ -450,7 +450,8 @@
" print(f\"epoch {epoch + 1}/{epoch_num}\")\n",
"\n",
" epoch_loss = 0\n",
" step = 1\n",
" step = 0\n",
" total_items = 0\n",
"\n",
" steps_per_epoch = len(train_ds) // train_loader.batch_size\n",
"\n",
Expand Down Expand Up @@ -478,11 +479,12 @@
" # and its internal optimisation strategy\n",
" optimizer.step()\n",
"\n",
" epoch_loss += loss.item()\n",
" print(f\"{step}/{len(train_ds) // train_loader.batch_size + 1}, training_loss: {loss.item():.4f}\")\n",
" epoch_loss += loss.item() * outputs.shape[0]\n",
" total_items += outputs.shape[0]\n",
" print(f\"{step + 1}/{len(train_ds) // train_loader.batch_size + 1}, training_loss: {loss.item():.4f}\")\n",
" step += 1\n",
"\n",
" epoch_loss /= step\n",
" epoch_loss /= total_items\n",
" epoch_loss_values.append(epoch_loss)\n",
" print(f\"epoch {epoch + 1} average loss: {epoch_loss:.4f}\")\n",
"\n",
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10 changes: 6 additions & 4 deletions MONAICore/3. End-To-End Workflow with MONAI.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -450,7 +450,8 @@
" print(f\"epoch {epoch + 1}/{epoch_num}\")\n",
"\n",
" epoch_loss = 0\n",
" step = 1\n",
" step = 0\n",
" total_items = 0\n",
"\n",
" steps_per_epoch = len(train_ds) // train_loader.batch_size\n",
"\n",
Expand Down Expand Up @@ -478,11 +479,12 @@
" # and its internal optimisation strategy\n",
" optimizer.step()\n",
"\n",
" epoch_loss += loss.item()\n",
" print(f\"{step}/{len(train_ds) // train_loader.batch_size + 1}, training_loss: {loss.item():.4f}\")\n",
" epoch_loss += loss.item() * outputs.shape[0]\n",
" total_items += outputs.shape[0]\n",
" print(f\"{step + 1}/{len(train_ds) // train_loader.batch_size + 1}, training_loss: {loss.item():.4f}\")\n",
" step += 1\n",
"\n",
" epoch_loss /= step\n",
" epoch_loss /= total_items\n",
" epoch_loss_values.append(epoch_loss)\n",
" print(f\"epoch {epoch + 1} average loss: {epoch_loss:.4f}\")\n",
"\n",
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8 changes: 6 additions & 2 deletions MONAICore/MONAI Bundle, MONAI Model Zoo, and Image Visualization.ipynb
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Expand Up @@ -109,7 +109,11 @@
"source": [
"## MONAI Bundle\n",
"\n",
"The objective of the MONAI bundle is to define a packaged model which includes the critical information necessary to allow users and programs to understand how the model is used and what purpose it is for. A bundle includes the stored weights of a single network as a pickled state dictionary plus optionally a Torchscript object and/or an ONNX object. Additional JSON files are included to store metadata about the model, information for constructing training, inference, and post-processing transform sequences, plain-text description, legal information, and other data the model creator wishes to include."
"MONAI bundles define a packaged model which includes the critical information necessary to allow users and programs to understand how the model is used and what purpose it is for. \n",
"\n",
"* Stored weights of a single network as a pickled state dictionary are included, plus optional Torchscript and/or ONNX object. \n",
"\n",
"* Additional JSON files store metadata about the model, information for constructing training, inference, and post-processing transform sequences, plain-text description, legal information, and other data the model creator wishes to include."
]
},
{
Expand Down Expand Up @@ -210,7 +214,7 @@
}
},
"source": [
"or alternatively, in `YAML` format (`demo_config.yaml`):\n",
"Alternatively, in `YAML` format (`demo_config.yaml`):\n",
"\n",
"```yaml\n",
"demo_net:\n",
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