instance_id stringlengths 15 28 | file_changes listlengths 1 66 | repo stringclasses 11
values | base_commit stringlengths 40 40 | problem_statement stringlengths 23 39.4k | patch stringlengths 252 140k |
|---|---|---|---|---|---|
Project-MONAI__MONAI-2112 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/compose.py:Compose.__init__",
"monai/transforms/compose.py:Compose.__call__",
"monai/transforms/compose.py:Compose.inverse"
],
"edited_modules": [
"m... | Project-MONAI/MONAI | 06fd8fe1c661c5b41e03539f983ed889bf8e67bf | ArrayDataset only applies same transform if transforms match
**Describe the bug**
Noticed when looking into https://github.com/Project-MONAI/MONAI/discussions/2052.
`ArrayDataset` gives matching results if `img_transform` and `label_transform` match each other. However results diverge when they don't match. At whic... | diff --git a/monai/transforms/compose.py b/monai/transforms/compose.py
--- a/monai/transforms/compose.py
+++ b/monai/transforms/compose.py
@@ -34,9 +34,9 @@
class Compose(Randomizable, InvertibleTransform):
"""
- ``Compose`` provides the ability to chain a series of calls together in a
- sequence. Each tr... |
Project-MONAI__MONAI-6977 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/bundle/config_item.py:ConfigItem.__repr__",
"monai/bundle/config_item.py:ConfigComponent.instantiate",
"monai/bundle/config_item.py:ConfigExpression.evaluate"
],
"edite... | Project-MONAI/MONAI | d4dc055ef2ac321c0e468e82f8a73d637f4463e5 | better error message when bundle config expression has errors
**Describe the bug**
the current error messages are not intuitive, e.g.:
```
self._resolve_one_item(id=d, waiting_list=waiting_list, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/monai/bundle/reference_resolver.py", line 163, in _resolve... | diff --git a/monai/bundle/config_item.py b/monai/bundle/config_item.py
--- a/monai/bundle/config_item.py
+++ b/monai/bundle/config_item.py
@@ -18,6 +18,7 @@
from abc import ABC, abstractmethod
from collections.abc import Mapping, Sequence
from importlib import import_module
+from pprint import pformat
from typing i... |
Project-MONAI__MONAI-890 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/handlers/checkpoint_saver.py:CheckpointSaver.exception_raised"
],
"edited_modules": [
"monai/handlers/checkpoint_saver.py:CheckpointSaver"
]
},
"file": "monai/han... | Project-MONAI/MONAI | 04e1c345fc840f5a1b6504ee5857d5a9feb27d84 | Ctrl+C does not cancel workflow model training.
**Describe the bug**
When executing a python script that uses a MONAI workflow, Ctrl+C in terminal does not cancel the script. Instead, the current epoch is skipped and training resumes at the next epoch.
**To Reproduce**
Steps to reproduce the behavior:
1. Execute ... | diff --git a/monai/handlers/checkpoint_saver.py b/monai/handlers/checkpoint_saver.py
--- a/monai/handlers/checkpoint_saver.py
+++ b/monai/handlers/checkpoint_saver.py
@@ -37,11 +37,14 @@ class CheckpointSaver:
name: identifier of logging.logger to use, if None, defaulting to ``engine.logger``.
file_pr... |
Project-MONAI__MONAI-459 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/post/dictionary.py:Activationsd.__init__",
"monai/transforms/post/dictionary.py:Activationsd.__call__",
"monai/transforms/post/dictionary.py:AsDiscreted.__init__",
... | Project-MONAI/MONAI | 105ce15f4f41278fbd11ea699b1847c59dede690 | Support to replace original keys in post-transform
**Is your feature request related to a problem? Please describe.**
If the `output_postfix` is None, the post transform should use the original keys to save memory.
| diff --git a/monai/transforms/post/dictionary.py b/monai/transforms/post/dictionary.py
--- a/monai/transforms/post/dictionary.py
+++ b/monai/transforms/post/dictionary.py
@@ -71,6 +71,7 @@ def __init__(self, keys, output_postfix="act", sigmoid=False, softmax=False, oth
output_postfix (str): the postfix str... |
Project-MONAI__MONAI-3384 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/apps/pathology/transforms/spatial/array.py:TileOnGrid.__call__"
],
"edited_modules": [
"monai/apps/pathology/transforms/spatial/array.py:TileOnGrid"
]
},
"file": ... | Project-MONAI/MONAI | 5adf30beb3581e951556fd8c4f027828bf367a70 | Update TileOnGrid backend
**Is your feature request related to a problem? Please describe.**
Update `TileOnGrid` to support input/output type of `torch.Tensor` and `numpy` while its backend is `numpy` only.
| diff --git a/monai/apps/pathology/transforms/spatial/array.py b/monai/apps/pathology/transforms/spatial/array.py
--- a/monai/apps/pathology/transforms/spatial/array.py
+++ b/monai/apps/pathology/transforms/spatial/array.py
@@ -17,6 +17,7 @@
from monai.config.type_definitions import NdarrayOrTensor
from monai.transf... |
Project-MONAI__MONAI-803 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/handlers/mean_dice.py:MeanDice.__init__"
],
"edited_modules": [
"monai/handlers/mean_dice.py:MeanDice"
]
},
"file": "monai/handlers/mean_dice.py"
},
{
"ch... | Project-MONAI/MONAI | 89857013e39beeb34b65ace1f082302d467de5cf | Add LogSoftmax option in dice.py
In the dice.py file we have options to add sigmoid or softmax to the output. We can also add LogSoftmax to the output to ensure numeric overflows dont take place.
Either we can replace the softmax operation by LogSoftmax or have both options available.
@wyli @Nic-Ma
| diff --git a/monai/handlers/mean_dice.py b/monai/handlers/mean_dice.py
--- a/monai/handlers/mean_dice.py
+++ b/monai/handlers/mean_dice.py
@@ -33,6 +33,7 @@ def __init__(
to_onehot_y: bool = False,
mutually_exclusive: bool = False,
sigmoid: bool = False,
+ other_act: Optional[Callable]... |
Project-MONAI__MONAI-1690 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "monai/__init__.py"
}
] | Project-MONAI/MONAI | 380f042dec9c55ba1a5ab241ae6b1a7b3e2b07fb | Pycharm can not find declarication to go
In `https://github.com/Project-MONAI/tutorials/tree/master/3d_segmentation/challenge_baseline`, Pycharm can not track the usage of some submodules.
To be specific, when I use "Ctrl+ LeftClick" to try to jump to the source file of `monai.engines.SupervisedEvaluator`, Pycharm s... | diff --git a/monai/__init__.py b/monai/__init__.py
--- a/monai/__init__.py
+++ b/monai/__init__.py
@@ -44,3 +44,19 @@
# load all modules, this will trigger all export decorations
load_submodules(sys.modules[__name__], True, exclude_pattern=excludes)
+
+__all__ = [
+ "apps",
+ "config",
+ "data",
+ "engi... |
Project-MONAI__MONAI-5560 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/apps/pathology/transforms/post/array.py:HoVerNetNuclearTypePostProcessing.__call__"
],
"edited_modules": [
"monai/apps/pathology/transforms/post/array.py:HoVerNetNuclearTypePos... | Project-MONAI/MONAI | a8f67e4278d46b49a87488a41ba38431883e8907 | Binary prediction bug in `HoVerNetNuclearTypePostProcessing`
**Describe the bug**
Now in `HoVerNetNuclearTypePostProcessing`, if set `return_binary` to True, it will change `inst_pred` in place which will affect instance map prediction.
https://github.com/Project-MONAI/MONAI/blob/72130602340847e15f2042b2bb1b64f6f46ee... | diff --git a/monai/apps/pathology/transforms/post/array.py b/monai/apps/pathology/transforms/post/array.py
--- a/monai/apps/pathology/transforms/post/array.py
+++ b/monai/apps/pathology/transforms/post/array.py
@@ -12,6 +12,7 @@
from typing import Callable, Dict, List, Optional, Sequence, Tuple, Union
import numpy ... |
Project-MONAI__MONAI-3094 | [
{
"changes": {
"added_entities": [
"monai/transforms/intensity/array.py:RandGibbsNoise.randomize",
"monai/transforms/intensity/array.py:RandKSpaceSpikeNoise.randomize"
],
"added_modules": null,
"edited_entities": [
"monai/transforms/intensity/array.py:RandGaussian... | Project-MONAI/MONAI | 3c8cc78b9d79288fad611b9fda8d8288ca82a291 | Reduce code duplication -- Random dictionary transforms that can't call their array version
We have both array and dictionary transforms. In a lot of cases, our dictionary transforms include a for loop that repeatedly call the matching array transform. However, because most random array transforms have something like t... | diff --git a/monai/transforms/intensity/array.py b/monai/transforms/intensity/array.py
--- a/monai/transforms/intensity/array.py
+++ b/monai/transforms/intensity/array.py
@@ -86,6 +86,7 @@ class RandGaussianNoise(RandomizableTransform):
prob: Probability to add Gaussian noise.
mean: Mean or “centre” o... |
Project-MONAI__MONAI-2104 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/croppad/dictionary.py:RandWeightedCropd.__init__",
"monai/transforms/croppad/dictionary.py:RandWeightedCropd.__call__",
"monai/transforms/croppad/dictionary.py:RandCropB... | Project-MONAI/MONAI | 41488339c27137929ad33c83a2e4e222337caf4b | Need to deepcopy data in RandCropByPosNegLabeld transform
**Describe the bug**
Currently, when we crop samples in `RandCropByPosNegLabeld` transform, it uses shallow copy for meta_data and other information, then if we change some value in a sample, all the samples are changed.
Need to use `deepcopy` for it, similar ... | diff --git a/monai/transforms/croppad/dictionary.py b/monai/transforms/croppad/dictionary.py
--- a/monai/transforms/croppad/dictionary.py
+++ b/monai/transforms/croppad/dictionary.py
@@ -664,6 +664,9 @@ class RandWeightedCropd(Randomizable, MapTransform):
If its components have non-positive values, the cor... |
Project-MONAI__MONAI-600 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"examples/segmentation_3d/unet_evaluation_array.py:main"
],
"edited_modules": [
"examples/segmentation_3d/unet_evaluation_array.py:main"
]
},
"file": "examples/segmentat... | Project-MONAI/MONAI | cc431b2fd108c44a02a69e3b56d3dc72a5d14f1f | Update MeanDice Handler
**Is your feature request related to a problem? Please describe.**
As @myron just updated our MeanDice metric, need to update the high level handler.
| diff --git a/examples/segmentation_3d/unet_evaluation_array.py b/examples/segmentation_3d/unet_evaluation_array.py
--- a/examples/segmentation_3d/unet_evaluation_array.py
+++ b/examples/segmentation_3d/unet_evaluation_array.py
@@ -25,7 +25,7 @@
from monai.networks.nets import UNet
from monai.data import create_test_i... |
Project-MONAI__MONAI-4876 | [
{
"changes": {
"added_entities": [
"monai/fl/client/monai_algo.py:compute_weight_diff",
"monai/fl/client/monai_algo.py:check_bundle_config"
],
"added_modules": [
"monai/fl/client/monai_algo.py:compute_weight_diff",
"monai/fl/client/monai_algo.py:check_bundle_con... | Project-MONAI/MONAI | aeebfd675180beffa5a9a28faa6b79a20b763249 | Support sending of weight differences in MonaiAlgo
**Is your feature request related to a problem? Please describe.**
Currently, MonaiAlgo only supports sending full model weights.
**Describe the solution you'd like**
Add an option to compute and return weight differences after local training.
**Describe altern... | diff --git a/monai/fl/client/monai_algo.py b/monai/fl/client/monai_algo.py
--- a/monai/fl/client/monai_algo.py
+++ b/monai/fl/client/monai_algo.py
@@ -10,6 +10,7 @@
# limitations under the License.
import logging
+import os
import sys
from typing import TYPE_CHECKING, Optional
@@ -20,8 +21,17 @@
from monai.bun... |
Project-MONAI__MONAI-2513 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/losses/focal_loss.py:FocalLoss.forward"
],
"edited_modules": [
"monai/losses/focal_loss.py:FocalLoss"
]
},
"file": "monai/losses/focal_loss.py"
}
] | Project-MONAI/MONAI | 0711e0421afc16da378ffe7e348578ff2b3881f2 | Focal Loss returning 0.0 with include_background=False (7/July)
**Describe the bug**
Focal Loss returns 0 for all entries when input consists of only one channel. Tried running the spleen 3D segmentation tutorial with `DiceFocalLoss(include_background=False)`. Printing out dice and focal loss separately shows the prob... | diff --git a/monai/losses/focal_loss.py b/monai/losses/focal_loss.py
--- a/monai/losses/focal_loss.py
+++ b/monai/losses/focal_loss.py
@@ -22,7 +22,7 @@
class FocalLoss(_Loss):
"""
- Reimplementation of the Focal Loss described in:
+ Reimplementation of the Focal Loss (with a build-in sigmoid activation) ... |
Project-MONAI__MONAI-4168 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/bundle/reference_resolver.py:ReferenceResolver._resolve_one_item",
"monai/bundle/reference_resolver.py:ReferenceResolver.match_refs_pattern",
"monai/bundle/reference_resolver.py:Re... | Project-MONAI/MONAI | 639392725fe9bd300e698e7f93e8369d5a463cb3 | Need to enhance the logic control of bundle config
**Is your feature request related to a problem? Please describe.**
There are 2 missing features of the logic control in bundle `run` script:
1. Currently, we have key `_requires_` to execute some logic before instantiation of the component, but if the component has o... | diff --git a/monai/bundle/reference_resolver.py b/monai/bundle/reference_resolver.py
--- a/monai/bundle/reference_resolver.py
+++ b/monai/bundle/reference_resolver.py
@@ -134,7 +134,7 @@ def _resolve_one_item(self, id: str, waiting_list: Optional[Set[str]] = None, **
and v.is_import_statement(v.get_con... |
Project-MONAI__MONAI-5254 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/utils.py:compute_shape_offset"
],
"edited_modules": [
"monai/data/utils.py:compute_shape_offset"
]
},
"file": "monai/data/utils.py"
}
] | Project-MONAI/MONAI | 5b3b74143f9c8b985974e583b0a6f4029eef50e1 | `SpacingD` transform bug for certain affine input
I use the `SpacingD` transforms after `LoadImageD` and `AddChannelD`. I read in a nifti file of shape [368, 336, 368] , the input to the `spacingD` [1, 368, 336, 368]. The outputs of spacingD is a matrix with zeros.
I followed the trace and the last time I see non-... | diff --git a/monai/data/utils.py b/monai/data/utils.py
--- a/monai/data/utils.py
+++ b/monai/data/utils.py
@@ -875,17 +875,19 @@ def compute_shape_offset(
corners_out = inv_mat @ corners
corners_out = corners_out[:-1] / corners_out[-1]
out_shape = np.round(corners_out.ptp(axis=1)) if scale_extent else np... |
Project-MONAI__MONAI-2344 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/networks/blocks/upsample.py:UpSample.__init__"
],
"edited_modules": [
"monai/networks/blocks/upsample.py:UpSample"
]
},
"file": "monai/networks/blocks/upsample.py... | Project-MONAI/MONAI | 6476cee7c16cce81278c4555f5f25ecd02181d31 | UpSample module does not support `size` parameter for `nontrainable` mode
The `size` parameter is used to specify the spatial size of the output for `nontrainable` mode ( see: https://pytorch.org/docs/stable/generated/torch.nn.Upsample.html). I think this parameter should be added into our current UpSample module.
| diff --git a/monai/networks/blocks/upsample.py b/monai/networks/blocks/upsample.py
--- a/monai/networks/blocks/upsample.py
+++ b/monai/networks/blocks/upsample.py
@@ -9,7 +9,7 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from typing import Optional, Sequ... |
Project-MONAI__MONAI-5950 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "monai/metrics/rocauc.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transf... | Project-MONAI/MONAI | 58c256eae2f1d21436a0b9c0dab5d989b8665e55 | Why the data shape are different through transform "spacingd.
### Discussed in https://github.com/Project-MONAI/MONAI/discussions/5934
<div type='discussions-op-text'>
<sup>Originally posted by **xxsxxsxxs666** February 3, 2023</sup>
![1675428782920](https://user-images.githubusercontent.com/61532031/21660830... | diff --git a/monai/metrics/rocauc.py b/monai/metrics/rocauc.py
--- a/monai/metrics/rocauc.py
+++ b/monai/metrics/rocauc.py
@@ -12,10 +12,13 @@
from __future__ import annotations
import warnings
-from typing import cast
+from typing import TYPE_CHECKING, cast
import numpy as np
-import numpy.typing as npt
+
+if T... |
Project-MONAI__MONAI-4819 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/meta_tensor.py:MetaTensor.ensure_torch_and_prune_meta"
],
"edited_modules": [
"monai/data/meta_tensor.py:MetaTensor"
]
},
"file": "monai/data/meta_tensor.py"... | Project-MONAI/MONAI | 9317d141541fde75640f2f372f5a9d5917dbad98 | Training on dicom images throws key errors: "0008|0005", "0008|1050" or similar
Hi all
I have been facing some problems training on DICOM images. In specific I found that training throws key errors on "0008|0005", "0008|1050", which conditional optional and optional.
The files can be found here:
http://www.rub... | diff --git a/monai/data/meta_tensor.py b/monai/data/meta_tensor.py
--- a/monai/data/meta_tensor.py
+++ b/monai/data/meta_tensor.py
@@ -18,6 +18,7 @@
import numpy as np
import torch
+import monai
from monai.config.type_definitions import NdarrayTensor
from monai.data.meta_obj import MetaObj, get_track_meta
from m... |
Project-MONAI__MONAI-6736 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/metrics/utils.py:get_mask_edges"
],
"edited_modules": [
"monai/metrics/utils.py:get_mask_edges"
]
},
"file": "monai/metrics/utils.py"
},
{
"changes": {
... | Project-MONAI/MONAI | a5dff5b7e4dfe3fa711e7b77b615d6b8177a0868 | cropforeground with margin>0
**Describe the bug**
```py
import numpy as np
import monai.transforms as mt
from monai.visualize import matshow3d
mask_gt = np.zeros((1, 100, 100), np.uint8)
mask_gt[0, 0:50] = 1
output = mt.CropForeground(margin=2)(mask_gt)
print("cropped size: ", output.shape)
matshow3d(outpu... | diff --git a/monai/metrics/utils.py b/monai/metrics/utils.py
--- a/monai/metrics/utils.py
+++ b/monai/metrics/utils.py
@@ -176,7 +176,7 @@ def get_mask_edges(
else: # pytorch subvoxel, maybe on gpu, but croppad boolean values on GPU is not supported
seg_pred, seg_gt, or_vol = convert_to_tensor(ch... |
Project-MONAI__MONAI-4745 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/utility/dictionary.py:ConcatItemsd.__call__"
],
"edited_modules": [
"monai/transforms/utility/dictionary.py:ConcatItemsd"
]
},
"file": "monai/transform... | Project-MONAI/MONAI | 9c12cd8aab54e31f7c87956ca6fc20573d2148ec | Unsupported data type in `ConcatItemsD`
**Is your feature request related to a problem? Please describe.**
`ConcatItemsD` only support numpy.ndarray and torch.Tensor now, which is incompatible with MetaTensor data type.
https://github.com/Project-MONAI/MONAI/blob/c45b3f05b00567f2fa0c2058b8c9eb01fef573c4/monai/transf... | diff --git a/monai/transforms/utility/dictionary.py b/monai/transforms/utility/dictionary.py
--- a/monai/transforms/utility/dictionary.py
+++ b/monai/transforms/utility/dictionary.py
@@ -929,7 +929,8 @@ def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> Dict[Hashable, N
class ConcatItemsd(MapTransform):
... |
Project-MONAI__MONAI-2487 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "monai/engines/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/engi... | Project-MONAI/MONAI | 11af59ae1875aefc96996689dd17388c572bd2ed | Inflexible score function of CheckpointSaver
https://github.com/Project-MONAI/MONAI/blob/9f9b63a7dc56d8b31d4fc8d34aae77865ba95947/monai/handlers/checkpoint_saver.py#L148-L160
Currently the `CheckpointSaver` saves the check point that has the largest score value. However, this is not desirable when a lower score indi... | diff --git a/monai/engines/__init__.py b/monai/engines/__init__.py
--- a/monai/engines/__init__.py
+++ b/monai/engines/__init__.py
@@ -16,6 +16,7 @@
GanKeys,
IterationEvents,
default_make_latent,
+ default_metric_cmp_fn,
default_prepare_batch,
engine_apply_transform,
get_devices_spec,
d... |
Project-MONAI__MONAI-7542 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/bundle/workflows.py:BundleWorkflow.__init__",
"monai/bundle/workflows.py:ConfigWorkflow.__init__"
],
"edited_modules": [
"monai/bundle/workflows.py:BundleWorkflow",
... | Project-MONAI/MONAI | c885100e951e5b7b1fedf5e9bc965201592e8541 | Add "properties_path" in `BundleWorkflow`
- Add "properties_path" in BundleWorkflow for user to add customized properties.
- Remove ignite based properties in the default properties, since after add `properties_path`, we can define package-specific properties.
| diff --git a/monai/bundle/workflows.py b/monai/bundle/workflows.py
--- a/monai/bundle/workflows.py
+++ b/monai/bundle/workflows.py
@@ -11,6 +11,7 @@
from __future__ import annotations
+import json
import os
import sys
import time
@@ -24,6 +25,7 @@
from monai.bundle.config_parser import ConfigParser
from monai... |
Project-MONAI__MONAI-907 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/inferers/utils.py:_get_scan_interval"
],
"edited_modules": [
"monai/inferers/utils.py:_get_scan_interval"
]
},
"file": "monai/inferers/utils.py"
}
] | Project-MONAI/MONAI | f2ea6fa7a75acc235037e91611638be6bf34188a | sliding_window_inference() in monai.inferers went wrong when roi_size=(M,N,1)
**Describe the bug**
sliding_window_inference() gives NaN when roi_size=(M,N,1)
**To Reproduce**
Steps to reproduce the behavior:
1. Go to sliding_window_inference() in monai.inferers
2. Go to the line: run
slices = dense_patch_slices... | diff --git a/monai/inferers/utils.py b/monai/inferers/utils.py
--- a/monai/inferers/utils.py
+++ b/monai/inferers/utils.py
@@ -164,14 +164,22 @@ def sliding_window_inference(
def _get_scan_interval(
image_size: Sequence[int], roi_size: Sequence[int], num_spatial_dims: int, overlap: float
) -> Tuple[int, ...]:
- ... |
Project-MONAI__MONAI-6943 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/image_reader.py:ITKReader.read",
"monai/data/image_reader.py:PydicomReader._get_meta_dict",
"monai/data/image_reader.py:PydicomReader._get_affine"
],
"edited_modul... | Project-MONAI/MONAI | 02e7b795f4fcf62aab0bb029c814970fd50840ef | Get error when reading dicom series with itk backend
**Describe the bug**
When reading the dicom series with LoadImage(itk backend) in MONAI transforms, it reported a bug shown below.
It only shows errors when there is only one file in the folder.
```
HDF5-DIAG: Error detected in HDF5 (1.12.1) thread 0:
#000: ... | diff --git a/monai/data/image_reader.py b/monai/data/image_reader.py
--- a/monai/data/image_reader.py
+++ b/monai/data/image_reader.py
@@ -244,6 +244,7 @@ def read(self, data: Sequence[PathLike] | PathLike, **kwargs):
series_identifier = series_uid[0] if not self.series_name else self.series_name
... |
Project-MONAI__MONAI-4775 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/utils_pytorch_numpy_unification.py:percentile"
],
"edited_modules": [
"monai/transforms/utils_pytorch_numpy_unification.py:percentile"
]
},
"file": "mo... | Project-MONAI/MONAI | 83ec15685ead52f5b0c69019d88a160f60866cce | pytorch numpy unification error
**Describe the bug**
The following code works in 0.9.0 but not in 0.9.1. It gives the following exception:
```
> result = torch.quantile(x, q / 100.0, dim=dim, keepdim=keepdim)
E RuntimeError: quantile() q tensor must be same dtype as the input tensor
../../.... | diff --git a/monai/transforms/utils_pytorch_numpy_unification.py b/monai/transforms/utils_pytorch_numpy_unification.py
--- a/monai/transforms/utils_pytorch_numpy_unification.py
+++ b/monai/transforms/utils_pytorch_numpy_unification.py
@@ -107,8 +107,8 @@ def percentile(
if isinstance(x, np.ndarray):
resul... |
Project-MONAI__MONAI-6080 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/meta_tensor.py:MetaTensor.peek_pending_affine"
],
"edited_modules": [
"monai/data/meta_tensor.py:MetaTensor"
]
},
"file": "monai/data/meta_tensor.py"
},
... | Project-MONAI/MONAI | 01b6d70b313a0faf002b0203ba87df8e8e80b8d7 | review and implement transform functionals in dev
**Is your feature request related to a problem? Please describe.**
part of #4855
this is to track the progress of implementing transform functionals from the prototype defined in #5860, for logically three parts
- [x] minor utility enhancements in
- [x] monai.d... | diff --git a/monai/data/meta_tensor.py b/monai/data/meta_tensor.py
--- a/monai/data/meta_tensor.py
+++ b/monai/data/meta_tensor.py
@@ -484,6 +484,8 @@ def peek_pending_shape(self):
def peek_pending_affine(self):
res = self.affine
r = len(res) - 1
+ if r not in (2, 3):
+ warnings... |
Project-MONAI__MONAI-2784 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/networks/nets/densenet.py:_DenseLayer.__init__",
"monai/networks/nets/densenet.py:_DenseBlock.__init__",
"monai/networks/nets/densenet.py:_Transition.__init__",
"monai/netw... | Project-MONAI/MONAI | 4801ecfa6568acb577d1ebf59fb506498aeab775 | Make normalization type in DenseNet configurable
**Is your feature request related to a problem? Please describe.**
BatchNorm is sometimes not optimal for certain applications, e.g. federated learning.
**Describe the solution you'd like**
Please make the normalization type in DenseNet implementation configurable t... | diff --git a/monai/networks/nets/densenet.py b/monai/networks/nets/densenet.py
--- a/monai/networks/nets/densenet.py
+++ b/monai/networks/nets/densenet.py
@@ -17,7 +17,8 @@
import torch.nn as nn
from torch.hub import load_state_dict_from_url
-from monai.networks.layers.factories import Conv, Dropout, Norm, Pool
+fr... |
Project-MONAI__MONAI-6662 | [
{
"changes": {
"added_entities": [
"monai/optimizers/lr_scheduler.py:WarmupCosineSchedule.get_lr"
],
"added_modules": null,
"edited_entities": [
"monai/optimizers/lr_scheduler.py:WarmupCosineSchedule.__init__"
],
"edited_modules": [
"monai/optimizers/l... | Project-MONAI/MONAI | 8bc25b93527fd79f5b450d51b63dbd8b0a7452e2 | `WarmupCosineSchedule` add `end_lr`
`LinearLR` and `ExponentialLR` already have the `end_lr` argument, It would definitely be useful in `WarmupCosineSchedule` too.
`WarmupCosineSchedule` add `end_lr`
`LinearLR` and `ExponentialLR` already have the `end_lr` argument, It would definitely be useful in `WarmupCosineSched... | diff --git a/monai/optimizers/lr_scheduler.py b/monai/optimizers/lr_scheduler.py
--- a/monai/optimizers/lr_scheduler.py
+++ b/monai/optimizers/lr_scheduler.py
@@ -68,6 +68,7 @@ def __init__(
optimizer: Optimizer,
warmup_steps: int,
t_total: int,
+ end_lr: float = 0.0,
cycles: ... |
Project-MONAI__MONAI-5656 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "monai/bundle/utils.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/handlers... | Project-MONAI/MONAI | 90f1893211835d91112ba5195ab5b3d746179ff8 | Close MLFlow run automatically when workflow is end
The MLFlow will start a [run](https://mlflow.org/docs/latest/tracking.html#where-runs-are-recorded) in the backend to record experiments' details like parameters, metrics and images. Currently, the mlflow handler works fine if just run one round of several epoch trai... | diff --git a/monai/bundle/scripts.py b/monai/bundle/scripts.py
--- a/monai/bundle/scripts.py
+++ b/monai/bundle/scripts.py
@@ -561,6 +561,7 @@ def run(
"run_name": "@run_name",
"iteration_log": True,
"output_transform": "$monai.handl... |
Project-MONAI__MONAI-1596 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/networks/nets/dynunet.py:DynUNet.__init__",
"monai/networks/nets/dynunet.py:DynUNet.check_deep_supr_num",
"monai/networks/nets/dynunet.py:DynUNet.forward",
"monai/networks/... | Project-MONAI/MONAI | 3bdf0c8be60b792e7a2ef064aa2a53ae98f48942 | DynUnet get_feature_maps() issue when using distributed training
**Describe the bug**
If we use `DistributedDataParallel` to wrap the network, calling the 'get_feature_maps' function will raise the following error:
![Screen Shot 2021-02-08 at 6 51 01 PM](https://user-images.githubusercontent.com/68361391/107210065-... | diff --git a/monai/networks/nets/dynunet.py b/monai/networks/nets/dynunet.py
--- a/monai/networks/nets/dynunet.py
+++ b/monai/networks/nets/dynunet.py
@@ -14,6 +14,7 @@
import torch
import torch.nn as nn
+from torch.nn.functional import interpolate
from monai.networks.blocks.dynunet_block import UnetBasicBlock, ... |
Project-MONAI__MONAI-5093 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/losses/contrastive.py:ContrastiveLoss.__init__",
"monai/losses/contrastive.py:ContrastiveLoss.forward"
],
"edited_modules": [
"monai/losses/contrastive.py:ContrastiveLo... | Project-MONAI/MONAI | 0af5e18fd5ce2e8733d22096da1cead3b7e6b65c | ContrastiveLoss with dynamic batchsize
**Is your feature request related to a problem? Please describe.**
When we instantiate an instance of type class `ContrastiveLoss` we need to pass in the parameter for `batch_size`. This assumes that the batch size remains constant all through the training(which is not always the... | diff --git a/monai/losses/contrastive.py b/monai/losses/contrastive.py
--- a/monai/losses/contrastive.py
+++ b/monai/losses/contrastive.py
@@ -9,6 +9,8 @@
# See the License for the specific language governing permissions and
# limitations under the License.
+from distutils.log import warn
+
import torch
from torc... |
Project-MONAI__MONAI-3913 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "monai/handlers/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/han... | Project-MONAI/MONAI | 4c2899a8f83db8fe34dfe9d89208c509abb9ecc8 | Improve `output_transform` for StatsHandler
**Is your feature request related to a problem? Please describe.**
Currently, we usually use `output_transform=lambda x: None` to avoid logging of every iteration for evaluator:
https://github.com/Project-MONAI/tutorials/blob/master/modules/engines/unet_training_dict.py#L12... | diff --git a/monai/handlers/__init__.py b/monai/handlers/__init__.py
--- a/monai/handlers/__init__.py
+++ b/monai/handlers/__init__.py
@@ -33,5 +33,5 @@
from .stats_handler import StatsHandler
from .surface_distance import SurfaceDistance
from .tensorboard_handlers import TensorBoardHandler, TensorBoardImageHandler,... |
Project-MONAI__MONAI-4729 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/apps/detection/transforms/dictionary.py:ConvertBoxModed.__call__",
"monai/apps/detection/transforms/dictionary.py:ConvertBoxToStandardModed.__call__",
"monai/apps/detection/transfo... | Project-MONAI/MONAI | fed6fc75612522e4a6d93d7215e2940d8c7a0181 | MetaTensor: re-enable full tests
**Is your feature request related to a problem? Please describe.**
Follow-up of prototype https://github.com/Project-MONAI/MONAI/pull/4371
This ticket is to track the necessary breaking changes on branch [feature/MetaTensor](https://github.com/Project-MONAI/MONAI/tree/feature/MetaTe... | diff --git a/monai/apps/detection/transforms/dictionary.py b/monai/apps/detection/transforms/dictionary.py
--- a/monai/apps/detection/transforms/dictionary.py
+++ b/monai/apps/detection/transforms/dictionary.py
@@ -15,7 +15,6 @@
Class names are ended with 'd' to denote dictionary-based transforms.
"""
from copy impo... |
Project-MONAI__MONAI-7163 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "docs/source/conf.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/handlers/m... | Project-MONAI/MONAI | cc20c9bee91379e10762a15dd0f48c3e78271eb3 | Error when build docs
```
WARNING: The default value for `navigation_with_keys` will change to `False` in the next release. If you wish to preserve the old behavior for your site, set `navigation_with_keys=True` in the `html_theme_options` dict in your `conf.py` file.Be aware that `navigation_with_keys = True` has neg... | diff --git a/docs/source/conf.py b/docs/source/conf.py
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -126,6 +126,7 @@ def generate_apidocs(*args):
{"name": "Twitter", "url": "https://twitter.com/projectmonai", "icon": "fab fa-twitter-square"},
],
"collapse_navigation": True,
+ "navigation... |
Project-MONAI__MONAI-6681 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/metrics/surface_dice.py:SurfaceDiceMetric._compute_tensor",
"monai/metrics/surface_dice.py:compute_surface_dice"
],
"edited_modules": [
"monai/metrics/surface_dice.py:S... | Project-MONAI/MONAI | 18daff1d8b26002b02de526cc19b92a9a4907f89 | extensions of the surface-based metric
**Is your feature request related to a problem? Please describe.**
Follow up of https://github.com/Project-MONAI/MONAI/pull/4050,
this is a feature request to extend the surface-based metric module for 3D, with the support of more detailed quantizations when computing local surf... | diff --git a/monai/metrics/surface_dice.py b/monai/metrics/surface_dice.py
--- a/monai/metrics/surface_dice.py
+++ b/monai/metrics/surface_dice.py
@@ -35,8 +35,9 @@ class SurfaceDiceMetric(CumulativeIterationMetric):
Computes the Normalized Surface Dice (NSD) for each batch sample and class of
predicted segme... |
Project-MONAI__MONAI-1922 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/nifti_saver.py:NiftiSaver.save",
"monai/data/nifti_saver.py:NiftiSaver.save_batch"
],
"edited_modules": [
"monai/data/nifti_saver.py:NiftiSaver"
]
},
... | Project-MONAI/MONAI | d9e68c887b66e1ba0c77c4740cc1680aebda04b2 | SaveImageD transform need to support list of dict data
**Is your feature request related to a problem? Please describe.**
Currently, several crop transforms may generate a batch of data, but the `SaveImageD` transform will save them with the same file name and overwrite, need an index or something to distinguish batch... | diff --git a/monai/data/nifti_saver.py b/monai/data/nifti_saver.py
--- a/monai/data/nifti_saver.py
+++ b/monai/data/nifti_saver.py
@@ -9,7 +9,7 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from typing import Dict, Optional, Union
+from typing import Dict... |
Project-MONAI__MONAI-3385 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/handlers/tensorboard_handlers.py:TensorBoardImageHandler.__init__",
"monai/handlers/tensorboard_handlers.py:TensorBoardImageHandler.__call__"
],
"edited_modules": [
"mo... | Project-MONAI/MONAI | 8c90c59db79ea7b367639a342c8aeae8055f5fbb | Add `frame_dim` to the matshow3d utility
**Is your feature request related to a problem? Please describe.**
Currently, for higher dimensional data (like `BCHWD`), `matshow3d` will expand to a list of frame images on the flattened `BCH` dim. Would be useful to add a `frame_dim` arg to support any dim.
| diff --git a/monai/handlers/tensorboard_handlers.py b/monai/handlers/tensorboard_handlers.py
--- a/monai/handlers/tensorboard_handlers.py
+++ b/monai/handlers/tensorboard_handlers.py
@@ -275,6 +275,7 @@ def __init__(
global_iter_transform: Callable = lambda x: x,
index: int = 0,
max_channels:... |
Project-MONAI__MONAI-1746 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/utility/array.py:DataStats.__init__",
"monai/transforms/utility/array.py:DataStats.__call__"
],
"edited_modules": [
"monai/transforms/utility/array.py:DataSt... | Project-MONAI/MONAI | 6d3bf2fb7910afcb656fed91eb1d337c61c40ac4 | inaccurate code coverage report for multiprocess executions
**Describe the bug**
code coverage reports can't track multiprocessing code executions properly
https://codecov.io/gh/Project-MONAI/MONAI/tree/master/tests
therefore:
- codecov gives some false positive alarms
- actual coverage rate is better than the rep... | diff --git a/monai/transforms/utility/array.py b/monai/transforms/utility/array.py
--- a/monai/transforms/utility/array.py
+++ b/monai/transforms/utility/array.py
@@ -14,6 +14,7 @@
"""
import logging
+import sys
import time
from typing import TYPE_CHECKING, Callable, Dict, List, Optional, Sequence, Tuple, Union
... |
Project-MONAI__MONAI-6874 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/apps/auto3dseg/data_analyzer.py:DataAnalyzer._check_data_uniformity",
"monai/apps/auto3dseg/data_analyzer.py:DataAnalyzer._get_all_case_stats"
],
"edited_modules": [
"m... | Project-MONAI/MONAI | e24b9698bf87edf6b5b78b372c3021ca217e7fb6 | DataAnalyzer with `histogram_only=True`
**Describe the bug**
using `DataAnalyzer` with `histogram_only=True` raises error:
```
2023-08-15 15:15:52,439 - INFO - Found 0 GPUs for data analyzing!
2023-08-15 15:15:52,441 - INFO - device=cuda:0 but CUDA device is not available, using CPU instead.
0%| ... | diff --git a/monai/apps/auto3dseg/data_analyzer.py b/monai/apps/auto3dseg/data_analyzer.py
--- a/monai/apps/auto3dseg/data_analyzer.py
+++ b/monai/apps/auto3dseg/data_analyzer.py
@@ -161,6 +161,8 @@ def _check_data_uniformity(keys: list[str], result: dict) -> bool:
"""
+ if DataStatsKeys.SUMMARY not... |
Project-MONAI__MONAI-3493 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/losses/deform.py:BendingEnergyLoss.__init__",
"monai/losses/deform.py:BendingEnergyLoss.forward"
],
"edited_modules": [
"monai/losses/deform.py:BendingEnergyLoss"
... | Project-MONAI/MONAI | 99276919551d6768f6f4a7da38f416f933041fd0 | Bending energy loss is not scale invariant
Bending energy loss is intended to be applied to a vector field to tell us something about the regularity of the image deformation that the vector field defines when interpreted as a displacement map. I think such a measure should not depend on the resolution of the images tha... | diff --git a/monai/losses/deform.py b/monai/losses/deform.py
--- a/monai/losses/deform.py
+++ b/monai/losses/deform.py
@@ -52,9 +52,12 @@ class BendingEnergyLoss(_Loss):
DeepReg (https://github.com/DeepRegNet/DeepReg)
"""
- def __init__(self, reduction: Union[LossReduction, str] = LossReduction.MEAN)... |
Project-MONAI__MONAI-4590 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/networks/blocks/convolutions.py:Convolution.__init__"
],
"edited_modules": [
"monai/networks/blocks/convolutions.py:Convolution"
]
},
"file": "monai/networks/bloc... | Project-MONAI/MONAI | ff9ff55dd9198dabcc31eebe3109332ea708b356 | Dropout is not firing in DynUNet class
Monai version 0.9.0
<img width="365" alt="image" src="https://user-images.githubusercontent.com/24542592/175794956-edd8e68a-e54a-4677-9bb4-987bec8d4f6d.png">
| diff --git a/monai/data/image_reader.py b/monai/data/image_reader.py
--- a/monai/data/image_reader.py
+++ b/monai/data/image_reader.py
@@ -398,11 +398,6 @@ class PydicomReader(ImageReader):
(for example, when using this reader with `monai.transforms.LoadImage`), please ensure that the argument
... |
Project-MONAI__MONAI-6910 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/bundle/workflows.py:ConfigWorkflow.__init__",
"monai/bundle/workflows.py:ConfigWorkflow.run"
],
"edited_modules": [
"monai/bundle/workflows.py:ConfigWorkflow"
]
... | Project-MONAI/MONAI | a4e4894dca25f5e87b9306abfc472805f92b69da | Add `MetaProterties` and update `load` API
Part of #6726
- Add `create_workflow`, which can create a `BundleWorkflow` by specifying config_file or workflow_name (which can support Python-based bundle)
- Add `MetaProterties`, now users can directly call meta information from an initialized `BundleWorkflow`
- Update... | diff --git a/monai/bundle/workflows.py b/monai/bundle/workflows.py
--- a/monai/bundle/workflows.py
+++ b/monai/bundle/workflows.py
@@ -12,6 +12,7 @@
from __future__ import annotations
import os
+import sys
import time
import warnings
from abc import ABC, abstractmethod
@@ -170,6 +171,7 @@ class ConfigWorkflow(Bu... |
Project-MONAI__MONAI-4511 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/metrics/generalized_dice.py:compute_generalized_dice"
],
"edited_modules": [
"monai/metrics/generalized_dice.py:compute_generalized_dice"
]
},
"file": "monai/metr... | Project-MONAI/MONAI | ed233d9b48bd71eb623cf9777ad9b60142c8ad66 | Wrong generalized dice score metric when denominator is 0 but prediction is non-empty
**Describe the bug**
When the denominator of the generalized dice score metric is zero, i.e., the ground-truth is empty, score should be 1 if the prediction is also empty and 0 otherwise. Right now, the output score is always 1.
*... | diff --git a/monai/metrics/generalized_dice.py b/monai/metrics/generalized_dice.py
--- a/monai/metrics/generalized_dice.py
+++ b/monai/metrics/generalized_dice.py
@@ -169,9 +169,15 @@ def compute_generalized_dice(
numer = 2.0 * (intersection * w).sum(dim=1)
denom = (denominator * w).sum(dim=1)
- # Comput... |
Project-MONAI__MONAI-3358 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/utility/array.py:ToTensor.__init__",
"monai/transforms/utility/array.py:ToTensor.__call__",
"monai/transforms/utility/array.py:EnsureType.__init__",
"monai/trans... | Project-MONAI/MONAI | f7e4cc3c8b8f348412641ea802bce2ee50c97506 | Missing `wrap_sequence` in `ToNumpy` and `EnsureType`
These two transforms (also for their dict versions) miss the parameter `wrap_sequence`.
| diff --git a/monai/transforms/utility/array.py b/monai/transforms/utility/array.py
--- a/monai/transforms/utility/array.py
+++ b/monai/transforms/utility/array.py
@@ -340,33 +340,48 @@ def __call__(self, img: NdarrayOrTensor, dtype: Optional[Union[DtypeLike, torch.
class ToTensor(Transform):
"""
Converts the... |
Project-MONAI__MONAI-4263 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/croppad/array.py:RandCropByPosNegLabel.__init__",
"monai/transforms/croppad/array.py:RandCropByPosNegLabel.randomize",
"monai/transforms/croppad/array.py:RandCropByPosNe... | Project-MONAI/MONAI | 0bbeb1e084d1c06a5f14af70ad340c798a1567aa | Some bug in `transforms.RandCropByPosNegLabeld` caused by `spatial_size`
**Describe the bug**
`RandCropByPosNegLabeld.spatial_size` will be wrongly replaced when the transform function applied to sequential data.
**To Reproduce**
```
from monai.transforms import RandCropByPosNegLabeld
import numpy as np
trans... | diff --git a/monai/transforms/croppad/array.py b/monai/transforms/croppad/array.py
--- a/monai/transforms/croppad/array.py
+++ b/monai/transforms/croppad/array.py
@@ -903,7 +903,7 @@ def __init__(
bg_indices: Optional[NdarrayOrTensor] = None,
allow_smaller: bool = False,
) -> None:
- self.... |
Project-MONAI__MONAI-6735 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/networks/nets/vitautoenc.py:ViTAutoEnc.__init__"
],
"edited_modules": [
"monai/networks/nets/vitautoenc.py:ViTAutoEnc"
]
},
"file": "monai/networks/nets/vitautoen... | Project-MONAI/MONAI | 4afa2ad317f8daa65c42a1aa13077401f5ec302d | `ViTAutoEnc` hard-codes output patch size to 4
**Describe the bug**
The `ViTAutoEnc` constructor hard-codes the output patch size to 4 in [this line](https://github.com/Project-MONAI/MONAI/blob/ae95bf920daad142bd8230580617a5e0a8d5d907/monai/networks/nets/vitautoenc.py#L103).
[Edit] I think `new_patch_size` needs t... | diff --git a/monai/networks/nets/vitautoenc.py b/monai/networks/nets/vitautoenc.py
--- a/monai/networks/nets/vitautoenc.py
+++ b/monai/networks/nets/vitautoenc.py
@@ -11,6 +11,7 @@
from __future__ import annotations
+import math
from collections.abc import Sequence
import torch
@@ -19,7 +20,7 @@
from monai.ne... |
Project-MONAI__MONAI-3566 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/image_reader.py:ITKReader.__init__",
"monai/data/image_reader.py:ITKReader.read"
],
"edited_modules": [
"monai/data/image_reader.py:ITKReader"
]
},
"... | Project-MONAI/MONAI | 9417ff217843db1cee7aef53b367cf1a7b21b7da | metadata when loading DICOM series
**Is your feature request related to a problem? Please describe.**
the image reader ignores metadata when loading from a directory using itk:
```py
import itk
from monai.transforms import LoadImage
loader = LoadImage(reader="ITKReader", pixel_type=itk.UC)
img, metadata = loade... | diff --git a/monai/data/image_reader.py b/monai/data/image_reader.py
--- a/monai/data/image_reader.py
+++ b/monai/data/image_reader.py
@@ -159,19 +159,27 @@ class ITKReader(ImageReader):
If ``False``, the spatial indexing follows the numpy convention;
otherwise, the spatial indexing convention... |
Project-MONAI__MONAI-6795 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/apps/pathology/inferers/inferer.py:SlidingWindowHoVerNetInferer.__call__"
],
"edited_modules": [
"monai/apps/pathology/inferers/inferer.py:SlidingWindowHoVerNetInferer"
]... | Project-MONAI/MONAI | 2a0ed971905005f62721e825b1cdc05e2d50acfd | predictor access of coordinates in `sliding_window_inference`
**Is your feature request related to a problem? Please describe.**
https://github.com/Project-MONAI/MONAI/blob/5feb353030e0bb204e21e1de338cd81b5972bb8a/monai/inferers/utils.py#L219-L223
`predictor` currently takes a batch of image windows as the primary ... | diff --git a/monai/apps/pathology/inferers/inferer.py b/monai/apps/pathology/inferers/inferer.py
--- a/monai/apps/pathology/inferers/inferer.py
+++ b/monai/apps/pathology/inferers/inferer.py
@@ -178,6 +178,7 @@ def __call__(
self.process_output,
self.buffer_steps,
self.buffer_dim,... |
Project-MONAI__MONAI-2848 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/intensity/array.py:RandCoarseDropout.__init__",
"monai/transforms/intensity/array.py:RandCoarseDropout.__call__"
],
"edited_modules": [
"monai/transforms/int... | Project-MONAI/MONAI | dd56514d28c5fbe08795676e150da0d1872f108c | Augmentation Transform | InCut & OutCut Dropping (ETA 08/27/21)
Dropping off randomly sized patches from inside the image and out the image where apart from them everything else gets dropped out.
| diff --git a/monai/transforms/intensity/array.py b/monai/transforms/intensity/array.py
--- a/monai/transforms/intensity/array.py
+++ b/monai/transforms/intensity/array.py
@@ -1633,8 +1633,9 @@ def _set_default_range(self, img: torch.Tensor) -> Sequence[Sequence[float]]:
class RandCoarseDropout(RandomizableTransform):
... |
Project-MONAI__MONAI-4977 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"monai/apps/detection/utils/ATSS_matcher.py:Matcher"
]
},
"file": "monai/apps/detection/utils/ATSS_matcher.py"
},
{
"changes": {
"added_entities"... | Project-MONAI/MONAI | 32af32c6400cfc6a91bf0932ba27ffdfc074c18c | handling indexerror for ConfigParser.get
I noticed that if we had a dictionary:
```python
config = {
'key1':
[{'key2_1': 1}, {'key2_2': 2}]
}
```
`config.get('key1#2')` will throw an error instead of returning a None because it only catches KeyError. I would like to suggest including `IndexError` so ... | diff --git a/monai/apps/detection/utils/ATSS_matcher.py b/monai/apps/detection/utils/ATSS_matcher.py
--- a/monai/apps/detection/utils/ATSS_matcher.py
+++ b/monai/apps/detection/utils/ATSS_matcher.py
@@ -74,7 +74,7 @@
"""
import logging
-from abc import ABC
+from abc import ABC, abstractmethod
from typing import Ca... |
Project-MONAI__MONAI-2326 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/image_reader.py:NibabelReader._get_meta_dict",
"monai/data/image_reader.py:NibabelReader._get_spatial_shape"
],
"edited_modules": [
"monai/data/image_reader.py:Nib... | Project-MONAI/MONAI | a961918457226bba8a744348be8fa1e5987ab46c | Saving NiFTI images with resampling raises memory error
Hello!
I have created the following pipeline and run it on some NiFTI images here (https://drive.google.com/drive/folders/1r2_0RTHFN8XfSLnSgMGYZuQXuhEpP4NC?usp=sharing). I would like to save the processed images as NiFTI because I am processing >10,000 images b... | diff --git a/monai/data/image_reader.py b/monai/data/image_reader.py
--- a/monai/data/image_reader.py
+++ b/monai/data/image_reader.py
@@ -404,7 +404,9 @@ def _get_meta_dict(self, img) -> Dict:
img: a Nibabel image object loaded from a image file.
"""
- return dict(img.header)
+ # ... |
Project-MONAI__MONAI-1011 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/croppad/array.py:CropForeground.__init__"
],
"edited_modules": [
"monai/transforms/croppad/array.py:CropForeground"
]
},
"file": "monai/transforms/crop... | Project-MONAI/MONAI | 74a89f8eb2e1aa376e32b481f1bf5ffe11caca92 | Anisotropic margin for CropForeground transforms
**Is your feature request related to a problem? Please describe.**
The current implementation of the CropForeground and CropForegroundd transforms only accept an integer as input for `margin`, so all dimensions get enlarged by the same amount. This does not allow for "a... | diff --git a/monai/transforms/croppad/array.py b/monai/transforms/croppad/array.py
--- a/monai/transforms/croppad/array.py
+++ b/monai/transforms/croppad/array.py
@@ -384,14 +384,17 @@ class CropForeground(Transform):
"""
def __init__(
- self, select_fn: Callable = lambda x: x > 0, channel_indices: O... |
Project-MONAI__MONAI-6271 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/networks/blocks/selfattention.py:SABlock.__init__",
"monai/networks/blocks/selfattention.py:SABlock.forward"
],
"edited_modules": [
"monai/networks/blocks/selfattention... | Project-MONAI/MONAI | bb4df37ab17e2e1fc136fd3a28ce3178506db654 | Upgrade base PyTorch docker to 23.03
**Is your feature request related to a problem? Please describe.**
As PyTorch 23.03 was released, and we plan to use it as the final base docker for MONAI 1.2.
https://catalog.ngc.nvidia.com/orgs/nvidia/containers/pytorch
Would be nice to upgrade the base docker and CI tests to 2... | diff --git a/monai/networks/blocks/selfattention.py b/monai/networks/blocks/selfattention.py
--- a/monai/networks/blocks/selfattention.py
+++ b/monai/networks/blocks/selfattention.py
@@ -25,13 +25,21 @@ class SABlock(nn.Module):
An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale <https://ar... |
Project-MONAI__MONAI-489 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"examples/classification_3d/densenet_training_dict.py:main"
],
"edited_modules": [
"examples/classification_3d/densenet_training_dict.py:main"
]
},
"file": "examples/cla... | Project-MONAI/MONAI | ae6acb1da8e62d049afe5682b89b058598647710 | Change `do_XXX`, `add_XXX` to `XXX` in losses and metrics
**Is your feature request related to a problem? Please describe.**
Now we used different arg name in `loss`, `metric` and `post_transform`, for example:
`do_sigmoid`, `add_sigmoid`, `sigmoid`.
Need to use `sigmoid` for all args, same as `argmax` and `softmax`... | diff --git a/examples/classification_3d/densenet_training_dict.py b/examples/classification_3d/densenet_training_dict.py
--- a/examples/classification_3d/densenet_training_dict.py
+++ b/examples/classification_3d/densenet_training_dict.py
@@ -132,7 +132,7 @@ def main():
acc_value = torch.eq(y_pred.ar... |
Project-MONAI__MONAI-6055 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/spatial/array.py:GridPatch.__init__",
"monai/transforms/spatial/array.py:GridPatch.filter_threshold",
"monai/transforms/spatial/array.py:GridPatch.__call__"
],
... | Project-MONAI/MONAI | 68074f07e4c04657f975cff2269ebe937f50e619 | GridPatch transform support for max num_patches while filtering
**Is your feature request related to a problem? Please describe.**
GridPatch is very useful to tile on the fly for a fixed number of patches. One usually uses an estimate of the average of number of tiles per slide. For slide with fewer tissue patches t... | diff --git a/monai/transforms/spatial/array.py b/monai/transforms/spatial/array.py
--- a/monai/transforms/spatial/array.py
+++ b/monai/transforms/spatial/array.py
@@ -68,7 +68,7 @@
optional_import,
)
from monai.utils.deprecate_utils import deprecated_arg
-from monai.utils.enums import GridPatchSort, PytorchPadMo... |
Project-MONAI__MONAI-763 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/utils.py:dense_patch_slices"
],
"edited_modules": [
"monai/data/utils.py:dense_patch_slices"
]
},
"file": "monai/data/utils.py"
}
] | Project-MONAI/MONAI | b37b9208077caccfeaacd1571d1452bb33b52b17 | Incorrect operation of dense_patch_slices
**Describe the bug**
I found that the sliding window inference function was much slower than expected. Looking into this, I found that the dense_patch_slices function is returning many duplicated slices for certain inputs.
**To Reproduce**
For example:
```
>>> x = dens... | diff --git a/monai/data/utils.py b/monai/data/utils.py
--- a/monai/data/utils.py
+++ b/monai/data/utils.py
@@ -20,7 +20,7 @@
from torch.utils.data._utils.collate import default_collate
import numpy as np
-from monai.utils import ensure_tuple_size, optional_import, NumpyPadMode, BlendMode
+from monai.utils import en... |
Project-MONAI__MONAI-1887 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/utils.py:list_data_collate"
],
"edited_modules": [
"monai/data/utils.py:list_data_collate"
]
},
"file": "monai/data/utils.py"
}
] | Project-MONAI/MONAI | 9f6ceebca87c06ec9fed8447791c9a7f3378ef0a | improve list_data_collate error messages
**Is your feature request related to a problem? Please describe.**
`list_data_collate` or the pytorch's `default_collate` may raise `RuntimeError` or `TypeError`, but the error messages are difficult to understand. This is a feature request to improve the error message especial... | diff --git a/monai/data/utils.py b/monai/data/utils.py
--- a/monai/data/utils.py
+++ b/monai/data/utils.py
@@ -15,7 +15,7 @@
import os
import pickle
import warnings
-from collections import defaultdict
+from collections import abc, defaultdict
from itertools import product, starmap
from pathlib import PurePath
fr... |
Project-MONAI__MONAI-4642 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/croppad/batch.py:PadListDataCollate.inverse"
],
"edited_modules": [
"monai/transforms/croppad/batch.py:PadListDataCollate"
]
},
"file": "monai/transfor... | Project-MONAI/MONAI | 99b9dd7cf0667113e56f0dd90d40699115048d59 | PadListDataCollate to support inverse MetaTensor
`PadListDataCollate.inverse` should support MetaTensor (as it's used in test time augmentation)
https://github.com/Project-MONAI/MONAI/blob/99b9dd7cf0667113e56f0dd90d40699115048d59/monai/transforms/croppad/batch.py#L114-L118
also the test cases are incomplete:
https... | diff --git a/monai/transforms/croppad/batch.py b/monai/transforms/croppad/batch.py
--- a/monai/transforms/croppad/batch.py
+++ b/monai/transforms/croppad/batch.py
@@ -19,6 +19,7 @@
import numpy as np
import torch
+from monai.data.meta_tensor import MetaTensor
from monai.data.utils import list_data_collate
from mo... |
Project-MONAI__MONAI-1093 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/intensity/array.py:NormalizeIntensity.__init__",
"monai/transforms/intensity/array.py:NormalizeIntensity._normalize",
"monai/transforms/intensity/array.py:NormalizeInten... | Project-MONAI/MONAI | ca1f27f60a7f01d2b1dd9e581f81edcdf304fd2d | divide std in NormalizeIntensity, but std could be 0
**Describe the bug**
In monai/transforms/intensity/array.py,
img[slices] = (img[slices] - np.mean(img[slices])) / np.std(img[slices])
But the np.std(img[slices]) could be 0 in some cases.
This will cause NaN.
**To Reproduce**
Steps to reproduce the behavior:
... | diff --git a/monai/transforms/intensity/array.py b/monai/transforms/intensity/array.py
--- a/monai/transforms/intensity/array.py
+++ b/monai/transforms/intensity/array.py
@@ -185,11 +185,11 @@ def __call__(self, img: np.ndarray) -> np.ndarray:
class NormalizeIntensity(Transform):
"""
- Normalize input based ... |
Project-MONAI__MONAI-5507 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/bundle/scripts.py:init_bundle"
],
"edited_modules": [
"monai/bundle/scripts.py:init_bundle"
]
},
"file": "monai/bundle/scripts.py"
}
] | Project-MONAI/MONAI | acffc2c7b1b9aaf29e1ee0710e9b17acee0dcac2 | update `init_bundle` to follow the latest model zoo license format
to make the initial bundle compatible with the model zoo, the `init_bundle` script should follow https://github.com/Project-MONAI/model-zoo/blob/dev/CONTRIBUTING.md#license-format
for example this file is not up-to-date:
https://github.com/Project-M... | diff --git a/monai/bundle/scripts.py b/monai/bundle/scripts.py
--- a/monai/bundle/scripts.py
+++ b/monai/bundle/scripts.py
@@ -799,6 +799,7 @@ def init_bundle(
bundle_dir: PathLike,
ckpt_file: Optional[PathLike] = None,
network: Optional[torch.nn.Module] = None,
+ dataset_license: bool = False,
m... |
Project-MONAI__MONAI-7137 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/post/array.py:RemoveSmallObjects.__init__",
"monai/transforms/post/array.py:RemoveSmallObjects.__call__"
],
"edited_modules": [
"monai/transforms/post/array.... | Project-MONAI/MONAI | 0a3cdd9f1403cbad057b96230840ee17cf430dbf | Add min_size_in_mm to RemoveSmallObjects transform
**Describe the solution you'd like**
RemoveSmallObjects is a great transform that is very much needed. However its arg is
min_size (int) – objects smaller than this size (in pixel) are removed.
Tumors and organs in medical are measured in mm^3 or CC^3. As radiolog... | diff --git a/monai/metrics/utils.py b/monai/metrics/utils.py
--- a/monai/metrics/utils.py
+++ b/monai/metrics/utils.py
@@ -261,11 +261,9 @@ def get_surface_distance(
- ``"euclidean"``, uses Exact Euclidean distance transform.
- ``"chessboard"``, uses `chessboard` metric in chamfer type of tran... |
Project-MONAI__MONAI-3560 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/dataset_summary.py:DatasetSummary.__init__",
"monai/data/dataset_summary.py:DatasetSummary.collect_meta_data",
"monai/data/dataset_summary.py:DatasetSummary.get_target_spacing... | Project-MONAI/MONAI | ba23afdd95e0d1ab0f9d17e43857f55897f54c1c | Enhance `DatasetSummary` for several points
**Is your feature request related to a problem? Please describe.**
Thanks for @dongyang0122 's great work to develop `DatasetSummary`, would be nice to enhance the below items:
1. It only has `meta_key_postfix` arg, missed `meta_key` to be consistent with other MONAI module... | diff --git a/monai/data/dataset_summary.py b/monai/data/dataset_summary.py
--- a/monai/data/dataset_summary.py
+++ b/monai/data/dataset_summary.py
@@ -15,8 +15,11 @@
import numpy as np
import torch
+from monai.config import KeysCollection
from monai.data.dataloader import DataLoader
from monai.data.dataset import... |
Project-MONAI__MONAI-3690 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/engines/workflow.py:Workflow.run"
],
"edited_modules": [
"monai/engines/workflow.py:Workflow"
]
},
"file": "monai/engines/workflow.py"
}
] | Project-MONAI/MONAI | 50c201c17e526a34240f20ca4512763baf9c94d0 | Skip workflow run if no data provided
**Is your feature request related to a problem? Please describe.**
Feature request from @SachidanandAlle :
Earlier we were not able to support zero input for validation, when there is no items for validation, we like to skip the evaluator.
can we add that fix if it's not there? ... | diff --git a/monai/engines/workflow.py b/monai/engines/workflow.py
--- a/monai/engines/workflow.py
+++ b/monai/engines/workflow.py
@@ -272,6 +272,13 @@ def run(self) -> None:
Execute training, validation or evaluation based on Ignite Engine.
"""
+ if self.state.epoch_length == 0:
+ ... |
Project-MONAI__MONAI-1948 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/decathlon_datalist.py:_compute_path",
"monai/data/decathlon_datalist.py:_append_paths"
],
"edited_modules": [
"monai/data/decathlon_datalist.py:_compute_path",
... | Project-MONAI/MONAI | f1db865e6c6f8bfc780107dc8b479130b578b18a | Prepend path to "mask"
**Is your feature request related to a problem? Please describe.**
`decathlon_dataloader.py` only prepend `base_dir` path to "image" and if it's segmentation to "label". However, if we have a "mask" entry it is not prepended by `base_dir`.
https://github.com/Project-MONAI/MONAI/blob/master/mona... | diff --git a/monai/data/decathlon_datalist.py b/monai/data/decathlon_datalist.py
--- a/monai/data/decathlon_datalist.py
+++ b/monai/data/decathlon_datalist.py
@@ -17,34 +17,43 @@
@overload
-def _compute_path(base_dir: str, element: str) -> str:
+def _compute_path(base_dir: str, element: str, check_path: bool = Fal... |
Project-MONAI__MONAI-2170 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/handlers/segmentation_saver.py:SegmentationSaver.__init__",
"monai/handlers/segmentation_saver.py:SegmentationSaver.__call__"
],
"edited_modules": [
"monai/handlers/seg... | Project-MONAI/MONAI | eca3f19182b9fcee0be7123728a9826cd382d152 | TransformInverter has `collate` arg but can't work
**Describe the bug**
Currently, the `TransformInverter` hander can't support collate that doesn't generate 1 list of data.
| diff --git a/monai/handlers/iteration_metric.py b/monai/handlers/iteration_metric.py
--- a/monai/handlers/iteration_metric.py
+++ b/monai/handlers/iteration_metric.py
@@ -31,6 +31,8 @@ class IterationMetric(Metric): # type: ignore[valid-type, misc] # due to option
Class for metrics that should be computed on ever... |
Project-MONAI__MONAI-4036 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/apps/pathology/data/datasets.py:PatchWSIDataset.__init__",
"monai/apps/pathology/data/datasets.py:SmartCachePatchWSIDataset.__init__",
"monai/apps/pathology/data/datasets.py:Masked... | Project-MONAI/MONAI | 541d7abdacb00aaf1c7d0a80aebf0cc204dd571f | Support for chosen level in `PatchWSIDataset`
**Is your feature request related to a problem? Please describe.**
Following up on #3995, user likes to be able to define the whole slide image `level` when using `PatchWSIDataset` in order to load patches at that `level`.
**Describe the solution you'd like**
For the s... | diff --git a/monai/apps/pathology/data/datasets.py b/monai/apps/pathology/data/datasets.py
--- a/monai/apps/pathology/data/datasets.py
+++ b/monai/apps/pathology/data/datasets.py
@@ -35,6 +35,7 @@ class PatchWSIDataset(Dataset):
transform: transforms to be executed on input data.
image_reader_name: th... |
Project-MONAI__MONAI-4159 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/bundle/scripts.py:ckpt_export"
],
"edited_modules": [
"monai/bundle/scripts.py:ckpt_export"
]
},
"file": "monai/bundle/scripts.py"
}
] | Project-MONAI/MONAI | 8f5c9924df73f6f3dbb222d6a1263d71b7abd0cd | Checkpoint Export Functionality Should Require Bundle Directory Path Only
**Is your feature request related to a problem? Please describe.**
Currently to export a bundle as a Torchscript file one has to specify the files to include individually, eg:
```bash
python -m monai.bundle ckpt_export network_def \
--f... | diff --git a/monai/bundle/scripts.py b/monai/bundle/scripts.py
--- a/monai/bundle/scripts.py
+++ b/monai/bundle/scripts.py
@@ -28,6 +28,7 @@
from monai.data import load_net_with_metadata, save_net_with_metadata
from monai.networks import convert_to_torchscript, copy_model_state
from monai.utils import check_parent_d... |
Project-MONAI__MONAI-5771 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/bundle/scripts.py:load"
],
"edited_modules": [
"monai/bundle/scripts.py:load"
]
},
"file": "monai/bundle/scripts.py"
}
] | Project-MONAI/MONAI | 8037fcdfb81a578b59966497f1184b8bc3215761 | Support `remove_prefix` in `monai.bundle.load`
| diff --git a/monai/bundle/scripts.py b/monai/bundle/scripts.py
--- a/monai/bundle/scripts.py
+++ b/monai/bundle/scripts.py
@@ -326,6 +326,7 @@ def load(
bundle_dir: Optional[PathLike] = None,
source: str = download_source,
repo: Optional[str] = None,
+ remove_prefix: Optional[str] = "monai_",
pro... |
Project-MONAI__MONAI-4847 | [
{
"changes": {
"added_entities": [
"monai/data/iterable_dataset.py:ShuffleBuffer.randomized_pop",
"monai/data/iterable_dataset.py:ShuffleBuffer.generate_item"
],
"added_modules": null,
"edited_entities": [
"monai/data/iterable_dataset.py:ShuffleBuffer.__iter__"
... | Project-MONAI/MONAI | ac3d4f97eb6bd22f360054f9d5475557360fe463 | ShuffleBuffer can not iterate twice
**Describe the bug**
`ShuffleBuffer` overwrites `self.data` on the first iteration and can not be iterated twice.
[`data` is originally set to the source data](https://github.com/Project-MONAI/MONAI/blob/e3b47fe62c5a63dd9f479499fe971211a70811ec/monai/data/iterable_dataset.py#L78)... | diff --git a/monai/data/iterable_dataset.py b/monai/data/iterable_dataset.py
--- a/monai/data/iterable_dataset.py
+++ b/monai/data/iterable_dataset.py
@@ -72,6 +72,25 @@ class ShuffleBuffer(Randomizable, IterableDataset):
every iter() call, refer to the PyTorch idea:
https://github.com/pytorch... |
Project-MONAI__MONAI-6147 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/image_writer.py:ITKWriter.__init__",
"monai/data/image_writer.py:ITKWriter.set_data_array",
"monai/data/image_writer.py:ITKWriter.create_backend_obj"
],
"edited_mo... | Project-MONAI/MONAI | 678b5124a74f32859d692d142728ca1f7fa98a25 | Inconsistent writing of Metadata. Loading + Saving results in different metadata.
**Describe the bug**
Using SaveImage after LoadImage results in image saved with different metadata.
**To Reproduce**
Steps to reproduce the behavior:
```
original2 = LoadImage(image_only=True)(original_file)
SaveImage(ou... | diff --git a/monai/data/image_writer.py b/monai/data/image_writer.py
--- a/monai/data/image_writer.py
+++ b/monai/data/image_writer.py
@@ -373,13 +373,14 @@ class ITKWriter(ImageWriter):
output_dtype: DtypeLike = None
channel_dim: int | None
- def __init__(self, output_dtype: DtypeLike = np.float32, affi... |
Project-MONAI__MONAI-1086 | [
{
"changes": {
"added_entities": [
"monai/transforms/croppad/array.py:RandSpatialCropSamples.set_random_state"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"monai/transforms/croppad/array.py:RandSpatialCropSamples"
]
},
"file"... | Project-MONAI/MONAI | 06fb95585a87332a5232c17ac9214d0d690978d9 | RandSpatialCropSamples should support `set_random_state`
**Describe the bug**
RandSpatialCropSamples currently doesn't set the random state of the underlying cropping instance
the transform will be non-deterministic
| diff --git a/monai/transforms/croppad/array.py b/monai/transforms/croppad/array.py
--- a/monai/transforms/croppad/array.py
+++ b/monai/transforms/croppad/array.py
@@ -347,6 +347,13 @@ def __init__(
self.num_samples = num_samples
self.cropper = RandSpatialCrop(roi_size, random_center, random_size)
+ ... |
Project-MONAI__MONAI-6158 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "monai/bundle/properties.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/bun... | Project-MONAI/MONAI | c30a5b9e9a33bb0670c2b10821aecd3a2ceb9f85 | MonaiAlgo's convert_global_weights broken for multi-gpu clients
**Describe the bug**
If the server initializes the model in a single-GPU/CPU environment, but clients use multi-gpu training, we get a key mismatch in this function.
```
2023-04-05 10:40:13,775 - WARNING - No global weights converted! Received weight ... | diff --git a/monai/bundle/properties.py b/monai/bundle/properties.py
--- a/monai/bundle/properties.py
+++ b/monai/bundle/properties.py
@@ -159,6 +159,11 @@
BundleProperty.REQUIRED: True,
BundlePropertyConfig.ID: "device",
},
+ "evaluator": {
+ BundleProperty.DESC: "inference / evaluatio... |
Project-MONAI__MONAI-5640 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/utils.py:is_supported_format"
],
"edited_modules": [
"monai/data/utils.py:is_supported_format"
]
},
"file": "monai/data/utils.py"
}
] | Project-MONAI/MONAI | 025c10751a1be596b3be9d0b64bb095e653804c3 | More robust `is_supported_format` suffix check
**Is your feature request related to a problem? Please describe.**
Sometimes the data I receive have uppercase suffixes (e.g., IMAGE.PNG), this could be recognized as the lowercase counterpart.
**Describe the solution you'd like**
Simply change this line
https://gith... | diff --git a/monai/data/utils.py b/monai/data/utils.py
--- a/monai/data/utils.py
+++ b/monai/data/utils.py
@@ -1099,8 +1099,8 @@ def is_supported_format(filename: Union[Sequence[PathLike], PathLike], suffixes:
"""
filenames: Sequence[PathLike] = ensure_tuple(filename)
for name in filenames:
- toke... |
Project-MONAI__MONAI-5423 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/networks/nets/attentionunet.py:AttentionLayer.__init__",
"monai/networks/nets/attentionunet.py:AttentionUnet.__init__",
"monai/networks/nets/attentionunet.py:AttentionUnet._get_bot... | Project-MONAI/MONAI | a209b06438343830e561a0afd41b1025516a8977 | RuntimeError with AttentionUNet
### Discussed in https://github.com/Project-MONAI/MONAI/discussions/5421
<div type='discussions-op-text'>
<sup>Originally posted by **njneeteson** October 27, 2022</sup>
I'm getting a RuntimeError when using the AttentionUnet in both 2D and 3D. This happens when training using a d... | diff --git a/monai/networks/nets/attentionunet.py b/monai/networks/nets/attentionunet.py
--- a/monai/networks/nets/attentionunet.py
+++ b/monai/networks/nets/attentionunet.py
@@ -143,12 +143,27 @@ def forward(self, g: torch.Tensor, x: torch.Tensor) -> torch.Tensor:
class AttentionLayer(nn.Module):
- def __init_... |
Project-MONAI__MONAI-6139 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/inferers/inferer.py:PatchInferer.__init__",
"monai/inferers/inferer.py:PatchInferer._batch_sampler"
],
"edited_modules": [
"monai/inferers/inferer.py:PatchInferer"
... | Project-MONAI/MONAI | 3b6b11a815b2de9e2b1bc1f1dbbca4e66189458f | Multi-threaded patch inference
Currently, Patch inference using `PatchInferer` supports multi-threading via dataloader, which is fine for most of our use cases since IO is occurring at datatloader and splitter components of patch inference just do the slicing of the already loaded image.
However, in the case of whole ... | diff --git a/monai/inferers/inferer.py b/monai/inferers/inferer.py
--- a/monai/inferers/inferer.py
+++ b/monai/inferers/inferer.py
@@ -22,6 +22,7 @@
from monai.apps.utils import get_logger
from monai.data.meta_tensor import MetaTensor
+from monai.data.thread_buffer import ThreadBuffer
from monai.inferers.merger im... |
Project-MONAI__MONAI-4721 | [
{
"changes": {
"added_entities": [
"monai/bundle/config_parser.py:ConfigParser.update"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"monai/bundle/config_parser.py:ConfigParser"
]
},
"file": "monai/bundle/config_parser.py"
},... | Project-MONAI/MONAI | 345b8ae72870828d23383013a2b4e222f8898b26 | Enhance bundle.read_config to pick either yaml or json automatically
https://github.com/Project-MONAI/model-zoo/tree/dev/models/pancreas_ct_dints_segmentation/configs
vs
https://github.com/Project-MONAI/model-zoo/tree/dev/models/spleen_ct_segmentation/configs
One using yaml and other using json.
If we want to u... | diff --git a/monai/bundle/config_parser.py b/monai/bundle/config_parser.py
--- a/monai/bundle/config_parser.py
+++ b/monai/bundle/config_parser.py
@@ -178,11 +178,27 @@ def get(self, id: str = "", default: Optional[Any] = None):
def set(self, config: Any, id: str = ""):
"""
- Set config by ``id``... |
Project-MONAI__MONAI-1906 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/utility/array.py:ConvertToMultiChannelBasedOnBratsClasses.__call__"
],
"edited_modules": [
"monai/transforms/utility/array.py:ConvertToMultiChannelBasedOnBratsClasse... | Project-MONAI/MONAI | ca8481f6d43c571abc63c6f08e85e8fe95d541f6 | ConvertToMultiChannelBasedOnBratsClasses should support channel first input
**Describe the bug**
Currently, `ConvertToMultiChannelBasedOnBratsClasses` transform expects the input data has no channel dim, should also support channel-first data.
| diff --git a/monai/transforms/utility/array.py b/monai/transforms/utility/array.py
--- a/monai/transforms/utility/array.py
+++ b/monai/transforms/utility/array.py
@@ -659,6 +659,10 @@ class ConvertToMultiChannelBasedOnBratsClasses(Transform):
"""
def __call__(self, img: np.ndarray) -> np.ndarray:
+ #... |
Project-MONAI__MONAI-4716 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/meta_tensor.py:MetaTensor.update_meta",
"monai/data/meta_tensor.py:MetaTensor.get_array",
"monai/data/meta_tensor.py:MetaTensor.astype",
"monai/data/meta_tensor.py:Met... | Project-MONAI/MONAI | ec4c03115ba45b2e950103a24db22f16d54c8d40 | metatensor slicing should decollate applied operations
**Describe the bug**
```py
from monai.data import MetaTensor, list_data_collate
from monai.transforms import Resize
a = MetaTensor([[1.0, 2.0]])
a = Resize((1, 2))(a)
b = list_data_collate([a, a])
print(b[0]) # decollate, slicing
```
output:
```
tenso... | diff --git a/monai/data/meta_tensor.py b/monai/data/meta_tensor.py
--- a/monai/data/meta_tensor.py
+++ b/monai/data/meta_tensor.py
@@ -215,20 +215,13 @@ def update_meta(rets: Sequence, func, args, kwargs) -> Sequence:
# if using e.g., `batch[:, -1]` or `batch[..., -1]`, then the
... |
Project-MONAI__MONAI-2321 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/croppad/dictionary.py:RandWeightedCropd.__call__",
"monai/transforms/croppad/dictionary.py:RandCropByPosNegLabeld.__call__"
],
"edited_modules": [
"monai/tra... | Project-MONAI/MONAI | cbf252199a8a1aa48672012f48d18dfdbb94301c | preserving order of the keys when transforming data
**Is your feature request related to a problem? Please describe.**
https://github.com/Project-MONAI/tutorials/issues/223
Packages such as Catalyst use the first item of the data dict to infer the batch size.
`self.batch_size = next(iter(batch.values())).shap... | diff --git a/monai/transforms/croppad/dictionary.py b/monai/transforms/croppad/dictionary.py
--- a/monai/transforms/croppad/dictionary.py
+++ b/monai/transforms/croppad/dictionary.py
@@ -855,7 +855,8 @@ def __call__(self, data: Mapping[Hashable, np.ndarray]) -> List[Dict[Hashable, n
self.randomize(d[self.w_key... |
Project-MONAI__MONAI-1010 | [
{
"changes": {
"added_entities": [
"monai/apps/datasets.py:DecathlonDataset.get_properties"
],
"added_modules": null,
"edited_entities": [
"monai/apps/datasets.py:DecathlonDataset.__init__"
],
"edited_modules": [
"monai/apps/datasets.py:DecathlonDatase... | Project-MONAI/MONAI | f5b81aa7b49d986bcf87884264e875ada7f481d1 | Add more properties in DecathlonDataset
**Is your feature request related to a problem? Please describe.**
We can load properties from the JSON config file of DecathlonDataset, for example: number of classes.
| diff --git a/monai/apps/datasets.py b/monai/apps/datasets.py
--- a/monai/apps/datasets.py
+++ b/monai/apps/datasets.py
@@ -14,8 +14,9 @@
from typing import Any, Callable, Dict, List, Optional, Sequence, Union
from monai.apps.utils import download_and_extract
-from monai.data import CacheDataset, load_decathlon_data... |
Project-MONAI__MONAI-682 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/utility/array.py:DataStats.__init__",
"monai/transforms/utility/array.py:DataStats.__call__"
],
"edited_modules": [
"monai/transforms/utility/array.py:DataSt... | Project-MONAI/MONAI | 8f3160a5434e656ac9b031411e975c719a68cbc8 | Add Tensor support to DataStats transform
**Is your feature request related to a problem? Please describe.**
Need to add `PyTorch Tensor` support for `DataStats` transform to debug post transforms.
| diff --git a/monai/transforms/utility/array.py b/monai/transforms/utility/array.py
--- a/monai/transforms/utility/array.py
+++ b/monai/transforms/utility/array.py
@@ -227,13 +227,15 @@ class DataStats(Transform):
"""
Utility transform to show the statistics of data for debug or analysis.
It can be insert... |
Project-MONAI__MONAI-5924 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/metrics/hausdorff_distance.py:compute_hausdorff_distance"
],
"edited_modules": [
"monai/metrics/hausdorff_distance.py:compute_hausdorff_distance"
]
},
"file": "mo... | Project-MONAI/MONAI | b59216458751db89598219f318f3ead2643fdf11 | Metrics fails or wrong output device with CUDA
**Describe the bug**
Hello, some metrics have bugs when used with CUDA tensors. In particular, Generalized Dice Score fails with the following error when both `y_pred` and `y` are on the same CUDA device.
`RuntimeError: Expected all tensors to be on the same device, b... | diff --git a/monai/metrics/hausdorff_distance.py b/monai/metrics/hausdorff_distance.py
--- a/monai/metrics/hausdorff_distance.py
+++ b/monai/metrics/hausdorff_distance.py
@@ -23,7 +23,7 @@
ignore_background,
is_binary_tensor,
)
-from monai.utils import MetricReduction
+from monai.utils import MetricReduction... |
Project-MONAI__MONAI-5854 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/bundle/config_item.py:ConfigComponent.resolve_module_name"
],
"edited_modules": [
"monai/bundle/config_item.py:ConfigComponent"
]
},
"file": "monai/bundle/config_... | Project-MONAI/MONAI | 6cb4ced0ea50b427a4065b4516be61b7a073abce | Parse callables (functions, methods) similarly to objects
**Is your feature request related to a problem? Please describe.**
Support for functions/methods in config by making Monai call them instead of attempting to instantiate them.
```
calculate:
_target_: "math.isclose"
a: 0.001
b: 0.002
```
**... | diff --git a/monai/bundle/config_item.py b/monai/bundle/config_item.py
--- a/monai/bundle/config_item.py
+++ b/monai/bundle/config_item.py
@@ -236,7 +236,7 @@ def resolve_module_name(self):
config = dict(self.get_config())
target = config.get("_target_")
if not isinstance(target, str):
- ... |
Project-MONAI__MONAI-3478 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "monai/config/type_definitions.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mon... | Project-MONAI/MONAI | cb70e135c721aec3c712d48068b7416448029bb3 | Support string dtype in transforms when processing Tensor data
**Is your feature request related to a problem? Please describe.**
As numpy array can accept the `dtype` arg in string, so many previous programs use `dtype="float32"` in the MONAI transforms. If we put `ToTensor` before the transform to make it work on GP... | diff --git a/monai/config/type_definitions.py b/monai/config/type_definitions.py
--- a/monai/config/type_definitions.py
+++ b/monai/config/type_definitions.py
@@ -60,8 +60,8 @@
# container must be iterable.
IndexSelection = Union[Iterable[int], int]
-#: Type of datatypes: Adapted from https://github.com/numpy/numpy... |
Project-MONAI__MONAI-1946 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/handlers/checkpoint_loader.py:CheckpointLoader.__init__",
"monai/handlers/checkpoint_loader.py:CheckpointLoader.__call__"
],
"edited_modules": [
"monai/handlers/checkpo... | Project-MONAI/MONAI | 713490b82d2f5f23d7a077a052d64f2cd1e0cfd9 | Add `strict_shape` option to CheckpointLoader
**Is your feature request related to a problem? Please describe.**
Currently, we don't support the transfer-learning case that load a checkpoint with same layer names but different shape.
We can refer to below code:
```py
model_3 = get_model_with_3_classes()
state_dict... | diff --git a/monai/handlers/checkpoint_loader.py b/monai/handlers/checkpoint_loader.py
--- a/monai/handlers/checkpoint_loader.py
+++ b/monai/handlers/checkpoint_loader.py
@@ -13,6 +13,7 @@
from typing import TYPE_CHECKING, Dict, Optional
import torch
+import torch.nn as nn
from monai.utils import exact_version, ... |
Project-MONAI__MONAI-6090 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/image_reader.py:_stack_images",
"monai/data/image_reader.py:ITKReader.__init__",
"monai/data/image_reader.py:ITKReader.get_data",
"monai/data/image_reader.py:PydicomRe... | Project-MONAI/MONAI | 958aac78ab8130517638a47175571e081ae03aee | `ORIGINAL_CHANNEL_DIM` datatype for collate
**Describe the bug**
the `ORIGINAL_CHANNEL_DIM` field currently allows different datatypes
https://github.com/Project-MONAI/MONAI/blob/68074f07e4c04657f975cff2269ebe937f50e619/monai/data/image_reader.py#L307-L309
and this causes errors when collating multiple metatensor... | diff --git a/monai/data/image_reader.py b/monai/data/image_reader.py
--- a/monai/data/image_reader.py
+++ b/monai/data/image_reader.py
@@ -27,6 +27,7 @@
from monai.data.utils import (
affine_to_spacing,
correct_nifti_header_if_necessary,
+ is_no_channel,
is_supported_format,
orientation_ras_lps,... |
Project-MONAI__MONAI-3403 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/utils.py:correct_crop_centers"
],
"edited_modules": [
"monai/transforms/utils.py:correct_crop_centers"
]
},
"file": "monai/transforms/utils.py"
}
] | Project-MONAI/MONAI | d625b61104f952834a4ead5b10ba3c7a309ffa7a | inconsistent output types for `correct_crop_centers`
**Describe the bug**
```py
import torch
from monai.transforms.utils import correct_crop_centers
correct_crop_centers(
centers=[torch.tensor(1), torch.tensor(5), torch.tensor(0)],
spatial_shape=[2, 2, 2],
label_spatial_shape=[10, 10, 10])
# [te... | diff --git a/monai/transforms/utils.py b/monai/transforms/utils.py
--- a/monai/transforms/utils.py
+++ b/monai/transforms/utils.py
@@ -415,7 +415,7 @@ def correct_crop_centers(
allow_smaller: bool = False,
):
"""
- Utility to correct the crop center if the crop size is bigger than the image size.
+ Uti... |
Project-MONAI__MONAI-2446 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/dataset.py:SmartCacheDataset.__init__"
],
"edited_modules": [
"monai/data/dataset.py:SmartCacheDataset"
]
},
"file": "monai/data/dataset.py"
}
] | Project-MONAI/MONAI | 05b2da61d70324c2f02b5d72429ddb7cc171b9b9 | SmartCacheDataset modified input datalist
**Describe the bug**
Bug reported by an internal user:
If set `shuffle=True` in `SmartCacheDataset`, it will modify the input datalist in place, program to reproduce:
```py
data_list = list(np.array([i]) for i in range(5))
print("original datalist:", data_list)
SmartCache... | diff --git a/monai/data/dataset.py b/monai/data/dataset.py
--- a/monai/data/dataset.py
+++ b/monai/data/dataset.py
@@ -19,7 +19,7 @@
import threading
import time
import warnings
-from copy import deepcopy
+from copy import copy, deepcopy
from multiprocessing.pool import ThreadPool
from pathlib import Path
from ty... |
Project-MONAI__MONAI-2937 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/networks/nets/resnet.py:ResNet.__init__",
"monai/networks/nets/resnet.py:ResNet._downsample_basic_block",
"monai/networks/nets/resnet.py:ResNet._make_layer"
],
"edited_... | Project-MONAI/MONAI | 8651b622df76b75a9477538e985a14896f827150 | remove the hard-coded 3d constraint for resnet
**Is your feature request related to a problem? Please describe.**
the resnet implementation is hardcoded for 3d only while the network API support both 2d and 3d
https://github.com/Project-MONAI/MONAI/blob/62425d7d8809d129b4f35a51f425d02d325bd816/monai/networks/nets/res... | diff --git a/monai/networks/nets/resnet.py b/monai/networks/nets/resnet.py
--- a/monai/networks/nets/resnet.py
+++ b/monai/networks/nets/resnet.py
@@ -14,9 +14,10 @@
import torch
import torch.nn as nn
-import torch.nn.functional as F
from monai.networks.layers.factories import Conv, Norm, Pool
+from monai.networ... |
Project-MONAI__MONAI-1777 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/handlers/checkpoint_saver.py:CheckpointSaver.__init__"
],
"edited_modules": [
"monai/handlers/checkpoint_saver.py:CheckpointSaver"
]
},
"file": "monai/handlers/ch... | Project-MONAI/MONAI | 3406398d37926923da9253e018c933c8b92468cc | support greater_or_equal from ignite 0.4.4
**Is your feature request related to a problem? Please describe.**
In ignite 0.4.4, @vfdev-5 and I developed a new arg in CheckpointHandler `greater_or_equal`, which is a feature request from our interval research team.
https://github.com/pytorch/ignite/blob/master/ignite/ha... | diff --git a/monai/handlers/checkpoint_saver.py b/monai/handlers/checkpoint_saver.py
--- a/monai/handlers/checkpoint_saver.py
+++ b/monai/handlers/checkpoint_saver.py
@@ -60,6 +60,8 @@ class CheckpointSaver:
if `True`, then will save an object in the checkpoint file with key `checkpointer` to be consistent... |
Project-MONAI__MONAI-3107 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/utils/deprecated.py:deprecated_arg"
],
"edited_modules": [
"monai/utils/deprecated.py:deprecated_arg"
]
},
"file": "monai/utils/deprecated.py"
}
] | Project-MONAI/MONAI | 712d90ba845e3d486f91636da0a4d7eeabfb7e52 | `deprecated_arg` replacing name when deprecated argument is also passed.
**Describe the bug**
When constructing a class that has a deprecated argument and both the new and deprecated argument are passed the construction fails. This may happen, for example, when using other libraries that automatically construct the cl... | diff --git a/monai/utils/deprecated.py b/monai/utils/deprecated.py
--- a/monai/utils/deprecated.py
+++ b/monai/utils/deprecated.py
@@ -187,9 +187,15 @@ def _decorator(func):
@wraps(func)
def _wrapper(*args, **kwargs):
- if new_name is not None and name in kwargs:
+ if new_name ... |
Project-MONAI__MONAI-5880 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/bundle/config_item.py:ConfigComponent.instantiate"
],
"edited_modules": [
"monai/bundle/config_item.py:ConfigComponent"
]
},
"file": "monai/bundle/config_item.py"... | Project-MONAI/MONAI | e279463e3293471e9630a45df605ec6fc0b53f02 | Supporting callable functions in instantiate
**Is your feature request related to a problem? Please describe.**
Continuing discussion from #5854
Callable functions can form a key part of the instantiation pipeline. For example, several functions return object instances, and supporting this would be very useful.
... | diff --git a/monai/bundle/config_item.py b/monai/bundle/config_item.py
--- a/monai/bundle/config_item.py
+++ b/monai/bundle/config_item.py
@@ -21,7 +21,7 @@
from typing import Any
from monai.bundle.utils import EXPR_KEY
-from monai.utils import ensure_tuple, first, instantiate, optional_import, run_debug, run_eval
... |
Project-MONAI__MONAI-3735 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/post/array.py:Activations.__init__",
"monai/transforms/post/array.py:Activations.__call__",
"monai/transforms/post/array.py:AsDiscrete.__init__",
"monai/transfor... | Project-MONAI/MONAI | 2e498fdaf001c13493c71dc4400764453c7813e6 | Dimension is hardcoded for softmax/argmax for PostTransform
For both Dictionary and Array based post transform, the dimension is hardcoded.
Softmax:
https://github.com/Project-MONAI/MONAI/blob/dev/monai/transforms/post/array.py#L115
Argmax:
https://github.com/Project-MONAI/MONAI/blob/dev/monai/transforms/post/a... | diff --git a/monai/transforms/post/array.py b/monai/transforms/post/array.py
--- a/monai/transforms/post/array.py
+++ b/monai/transforms/post/array.py
@@ -55,7 +55,7 @@
class Activations(Transform):
"""
- Add activation operations to the model output, typically `Sigmoid` or `Softmax`.
+ Activation operati... |
Project-MONAI__MONAI-4736 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/networks/nets/vit.py:ViT.__init__"
],
"edited_modules": [
"monai/networks/nets/vit.py:ViT"
]
},
"file": "monai/networks/nets/vit.py"
}
] | Project-MONAI/MONAI | 953c7d4e30308cb6225911760772ec76ff71a063 | classification ViT have the final nn.Tanh()
### Discussed in https://github.com/Project-MONAI/MONAI/discussions/4580
<div type='discussions-op-text'>
<sup>Originally posted by **chris-clem** June 24, 2022</sup>
I was wondering why does the Vision Transformer (ViT) with `classification=True` have `nn.Tanh()` in t... | diff --git a/monai/networks/nets/vit.py b/monai/networks/nets/vit.py
--- a/monai/networks/nets/vit.py
+++ b/monai/networks/nets/vit.py
@@ -43,6 +43,7 @@ def __init__(
num_classes: int = 2,
dropout_rate: float = 0.0,
spatial_dims: int = 3,
+ post_activation="Tanh",
) -> None:
... |
Project-MONAI__MONAI-1829 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/transform.py:apply_transform"
],
"edited_modules": [
"monai/transforms/transform.py:apply_transform"
]
},
"file": "monai/transforms/transform.py"
},
... | Project-MONAI/MONAI | 8ddd09f4800e9ca5ec2c09f7d4f2a671dfc53add | apply_transform better error msg
**Is your feature request related to a problem? Please describe.**
follow up of https://github.com/Project-MONAI/MONAI/discussions/1784#discussioncomment-504257 the error message from the `apply_transform` function could be improved
- https://github.com/Project-MONAI/MONAI/blob/70388f... | diff --git a/monai/transforms/transform.py b/monai/transforms/transform.py
--- a/monai/transforms/transform.py
+++ b/monai/transforms/transform.py
@@ -16,7 +16,9 @@
from typing import Any, Callable, Dict, Generator, Hashable, Iterable, List, Optional, Tuple
import numpy as np
+import torch
+from monai import tran... |
Project-MONAI__MONAI-6523 | [
{
"changes": {
"added_entities": [
"monai/data/meta_tensor.py:MetaTensor.__format__"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"monai/data/meta_tensor.py:MetaTensor"
]
},
"file": "monai/data/meta_tensor.py"
}
] | Project-MONAI/MONAI | e084885c6d498ab02df8107d23aa159f742a2cdd | TypeError: unsupported format string passed to MetaTensor.__format__
**Describe the bug**
Not sure if the bug lies on this side, or on the side of PyTorch Lightning, but here it goes:
I'm using PyTorch Lightning to set up a simple training pipeline. When I use `pl.callbacks.EarlyStopping` with a `CacheDataset` and ... | diff --git a/monai/data/meta_tensor.py b/monai/data/meta_tensor.py
--- a/monai/data/meta_tensor.py
+++ b/monai/data/meta_tensor.py
@@ -590,6 +590,12 @@ def __str__(self):
"""
return f"meta{str(self.as_tensor())}"
+ def __format__(self, format_spec):
+ """
+ returns the output of pyt... |
Project-MONAI__MONAI-3289 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/croppad/batch.py:PadListDataCollate.__call__",
"monai/transforms/croppad/batch.py:PadListDataCollate.inverse"
],
"edited_modules": [
"monai/transforms/croppa... | Project-MONAI/MONAI | 64a3db5d1a00226fb8a71ff38789f10b1f74dfd0 | Random Intensity transforms for test-time augmentation
Hi,
Test-time augmentation is a helpful tool to use but it seems that currently only spatial transformations are included for TTA. Intensity transformations such as Random contrast are not invertible transforms and thus cannot be used in current TTA implementati... | diff --git a/monai/transforms/croppad/batch.py b/monai/transforms/croppad/batch.py
--- a/monai/transforms/croppad/batch.py
+++ b/monai/transforms/croppad/batch.py
@@ -20,10 +20,8 @@
import torch
from monai.data.utils import list_data_collate
-from monai.transforms.compose import Compose
from monai.transforms.cropp... |
Project-MONAI__MONAI-4583 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/apps/detection/transforms/box_ops.py:convert_mask_to_box"
],
"edited_modules": [
"monai/apps/detection/transforms/box_ops.py:convert_mask_to_box"
]
},
"file": "mo... | Project-MONAI/MONAI | 9c4710199b80178ad11f7dd74925eee3ae921863 | a bug in convert_mask_to_box, will fail for multi-class detection
**Describe the bug**
a bug in convert_mask_to_box, will fail for multi-class detection
**To Reproduce**
Steps to reproduce the behavior:
```
boxes_mask = numpy.asarray([[[-1, 0],[0, -1]]])
monai.apps.detection.transforms.box_ops.convert_mask_to_b... | diff --git a/monai/apps/detection/transforms/box_ops.py b/monai/apps/detection/transforms/box_ops.py
--- a/monai/apps/detection/transforms/box_ops.py
+++ b/monai/apps/detection/transforms/box_ops.py
@@ -305,11 +305,11 @@ def convert_mask_to_box(
boxes_b.append(min(fd_i)) # top left corner
for fd_... |
Project-MONAI__MONAI-5189 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/post/array.py:SobelGradients.__init__",
"monai/transforms/post/array.py:SobelGradients._get_kernel",
"monai/transforms/post/array.py:SobelGradients.__call__"
],
... | Project-MONAI/MONAI | fe60832699448012cfc116dd001a3cdbcae1a0a9 | Optional gradient direction in `SobelGradients`
`SobelGradients` currently calculate the gradients in both horizontal and vertical directions. However, there are use cases that only one of these gradients in required, so it will have redundant computations. It would be nice to be able to set `direction` and calculate t... | diff --git a/monai/transforms/post/array.py b/monai/transforms/post/array.py
--- a/monai/transforms/post/array.py
+++ b/monai/transforms/post/array.py
@@ -14,16 +14,17 @@
"""
import warnings
-from typing import Callable, Iterable, Optional, Sequence, Union
+from typing import Callable, Iterable, Optional, Sequence,... |
Project-MONAI__MONAI-5473 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/losses/image_dissimilarity.py:LocalNormalizedCrossCorrelationLoss.__init__",
"monai/losses/image_dissimilarity.py:LocalNormalizedCrossCorrelationLoss.forward"
],
"edited_module... | Project-MONAI/MONAI | 27362e482761985daac8d5ef732eb57b50c741f1 | LNCC loss instability for large kernel size
### Discussed in https://github.com/Project-MONAI/MONAI/discussions/3463
<div type='discussions-op-text'>
<sup>Originally posted by **ebrahimebrahim** December 9, 2021</sup>
I experienced some numerically unstable training while using LNCC loss to train a registration... | diff --git a/monai/losses/image_dissimilarity.py b/monai/losses/image_dissimilarity.py
--- a/monai/losses/image_dissimilarity.py
+++ b/monai/losses/image_dissimilarity.py
@@ -66,7 +66,7 @@ def __init__(
kernel_size: int = 3,
kernel_type: str = "rectangular",
reduction: Union[LossReduction, st... |
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