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 |
|---|---|---|---|---|---|
facebookresearch__hydra-1741 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hydra/_internal/utils.py:run_and_report"
],
"edited_modules": [
"hydra/_internal/utils.py:run_and_report",
"hydra/_internal/utils.py:FakeTracebackType"
]
},
"fi... | facebookresearch/hydra | 896be9086ca9b0fc2ad71ce97ab19b71b7c4f264 | [Bug] failure while sanitiainzg exception stack trace in some cases
In some scenarios, one of the insepected frames in the stack trace does not have a module, resulting in a failure to print the underlying error.
The following looks like it's resolving it:
```diff
++ hydra/_internal/utils.py
@@ -248,6 +248,8 @@... | diff --git a/hydra/_internal/utils.py b/hydra/_internal/utils.py
--- a/hydra/_internal/utils.py
+++ b/hydra/_internal/utils.py
@@ -7,7 +7,7 @@
from dataclasses import dataclass
from os.path import dirname, join, normpath, realpath
from traceback import print_exc, print_exception
-from types import FrameType
+from ty... |
facebookresearch__hydra-1601 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "hydra/_internal/grammar/utils.py"
},
{
"changes": {
"added_entities": [
"hydra/core/override_parser/overrides_visitor.py:HydraOverrideVi... | facebookresearch/hydra | ed267e00710bb6bf92d8904e4f9b2daa8a0e7770 | [Bug] Override grammar: quoted strings ending with a trailing backslash may trigger parsing errors
# ๐ Bug
## Description
The following override examples cause exceptions (note: there is escaping from the shell, so when using `\\` below, Hydra only sees `\`, and escaped quotes are also replaced, e.g. `\"` -> `"`):... | diff --git a/hydra/_internal/grammar/utils.py b/hydra/_internal/grammar/utils.py
--- a/hydra/_internal/grammar/utils.py
+++ b/hydra/_internal/grammar/utils.py
@@ -11,6 +11,13 @@
# Regular expression that matches any sequence of characters in `_ESC`.
_ESC_REGEX = re.compile(f"[{re.escape(_ESC)}]+")
+# Regular expres... |
facebookresearch__hydra-2011 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hydra/_internal/utils.py:run_and_report"
],
"edited_modules": [
"hydra/_internal/utils.py:run_and_report"
]
},
"file": "hydra/_internal/utils.py"
}
] | facebookresearch/hydra | 0570bb78637cb444aad4b2a28b4733da072a79e9 | [Bug] Hydra's exception formatting cannot handle exception raised in C extension
# ๐ Bug
## Description
I use `hydra` and `av`(PyAV), when `av` raise an error inside my hydra app, hydra cannot handle it correctly.
Because `inspect.getmodule` won't work for C extension.
```python
end: Optional[TracebackType] = tb
... | diff --git a/hydra/_internal/utils.py b/hydra/_internal/utils.py
--- a/hydra/_internal/utils.py
+++ b/hydra/_internal/utils.py
@@ -4,10 +4,10 @@
import logging.config
import os
import sys
+import traceback
import warnings
from dataclasses import dataclass
from os.path import dirname, join, normpath, realpath
-fro... |
facebookresearch__hydra-1006 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hydra/_internal/utils.py:_get_kwargs"
],
"edited_modules": [
"hydra/_internal/utils.py:_get_kwargs"
]
},
"file": "hydra/_internal/utils.py"
}
] | facebookresearch/hydra | 94bbaaad028678166896cf139f778240e02d0a69 | [Bug] String interpolation in instantiate is broken in hydra 1.0.2
# ๐ Bug
## Description
String interpolation does not work when the config node is used in instantiate().
## Checklist
- [x] I checked on the latest version of Hydra
- [x] I created a minimal repro
## To reproduce
** Minimal Code/Config s... | diff --git a/hydra/_internal/utils.py b/hydra/_internal/utils.py
--- a/hydra/_internal/utils.py
+++ b/hydra/_internal/utils.py
@@ -586,7 +586,9 @@ def _get_kwargs(config: Union[ObjectConf, DictConfig], **kwargs: Any) -> Any:
config_overrides = {}
passthrough = {}
for k, v in kwargs.items():
- if k... |
facebookresearch__hydra-729 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "hydra/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hydra/_internal/ut... | facebookresearch/hydra | 0ccc2aad1889b03dfebfdc74889662150127a3a9 | [Bug] Unable to instantiate classes with non primitive data types
# ๐ Bug
Continuing from issue https://github.com/facebookresearch/hydra/issues/650
I think the fix still doesn't seem to work for me. Here's a MWE that crashes for me, with the current master (0ccc2aad)
## To reproduce
```python
from omegaco... | diff --git a/hydra/__init__.py b/hydra/__init__.py
--- a/hydra/__init__.py
+++ b/hydra/__init__.py
@@ -5,6 +5,6 @@
from hydra.types import TaskFunction
# Source of truth for Hydra's version
-__version__ = "1.0.0rc1"
+__version__ = "1.0.0rc2"
__all__ = ["__version__", "MissingConfigException", "main", "utils", "T... |
facebookresearch__hydra-1695 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hydra/compose.py:compose"
],
"edited_modules": [
"hydra/compose.py:compose"
]
},
"file": "hydra/compose.py"
},
{
"changes": {
"added_entities": null,
... | facebookresearch/hydra | 8640a921f571275d2c48d787efbb76d45fc89d7f | strict flag was removed from the compose API without a prior deprecation
Strict config composition functionality has become the default in Hydra 1.0 (See https://hydra.cc/docs/upgrades/0.11_to_1.0/strict_mode_flag_deprecated).
This flag was completely removed in Hydra 1.1.0.
Unfortunately, the Compose API strict fl... | diff --git a/hydra/compose.py b/hydra/compose.py
--- a/hydra/compose.py
+++ b/hydra/compose.py
@@ -1,7 +1,9 @@
# Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved
+import warnings
+from textwrap import dedent
from typing import List, Optional
-from omegaconf import DictConfig, open_dict
+from ome... |
facebookresearch__hydra-1671 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hydra/_internal/defaults_list.py:_create_defaults_tree_impl"
],
"edited_modules": [
"hydra/_internal/defaults_list.py:_create_defaults_tree_impl"
]
},
"file": "hydra/_i... | facebookresearch/hydra | 2039df435ecfd7e382ffa07ddfaccf6e3972ab62 | [bug] Interpolation of `hydra/launcher` configuration name in defaults list causes `hydra.errors.ConfigCompositionException`
**Describe the bug**
By switching from version `1.0` to `1.1`, this configuration:
```yaml
defaults:
...
- override hydra/launcher: ${oc.env:HYDRA_LAUNCHER}
```
throws the following ... | diff --git a/hydra/_internal/defaults_list.py b/hydra/_internal/defaults_list.py
--- a/hydra/_internal/defaults_list.py
+++ b/hydra/_internal/defaults_list.py
@@ -543,13 +543,6 @@ def add_child(
for idx, dd in enumerate(children):
if isinstance(dd, InputDefault) and dd.is_interpolation():
- i... |
facebookresearch__hydra-1731 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hydra/_internal/defaults_list.py:_update_overrides"
],
"edited_modules": [
"hydra/_internal/defaults_list.py:_update_overrides"
]
},
"file": "hydra/_internal/defaults_l... | facebookresearch/hydra | 0ccf75f14db36bbedb8659102cc1b4b9bb32b8f2 | Overriding hydra config groups using legacy notation more than once is causing an error instead of a two deprecation warning
Example config:
```yaml
defaults:
- hydra/hydra_logging: colorlog
- hydra/job_logging: colorlog
```
| diff --git a/hydra/_internal/defaults_list.py b/hydra/_internal/defaults_list.py
--- a/hydra/_internal/defaults_list.py
+++ b/hydra/_internal/defaults_list.py
@@ -359,7 +359,12 @@ def _update_overrides(
continue
d.update_parent(parent.get_group_path(), parent.get_final_package())
- if see... |
facebookresearch__hydra-614 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hydra/core/hydra_config.py:HydraConfig.set_config"
],
"edited_modules": [
"hydra/core/hydra_config.py:HydraConfig"
]
},
"file": "hydra/core/hydra_config.py"
},
{
... | facebookresearch/hydra | 52361bdac705dd8f85cb15b75541630634e08e1d | Option to access hydra configs from interpolation
The hydra config node is removed from the tree before the program stats, which makes it impossible to rely on it at runtime.
The reason it's removed is that otherwise the user config would be very large even for a simple program.
That config however is still available... | diff --git a/hydra/core/hydra_config.py b/hydra/core/hydra_config.py
--- a/hydra/core/hydra_config.py
+++ b/hydra/core/hydra_config.py
@@ -15,7 +15,7 @@ def set_config(self, cfg: DictConfig) -> None:
assert cfg is not None
OmegaConf.set_readonly(cfg.hydra, True)
assert OmegaConf.get_type(cfg,... |
facebookresearch__hydra-1551 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hydra/_internal/defaults_list.py:_create_defaults_tree_impl"
],
"edited_modules": [
"hydra/_internal/defaults_list.py:_create_defaults_tree_impl"
]
},
"file": "hydra/_i... | facebookresearch/hydra | 36f125ab76dee432db7e2fc9af0bba5e450a4056 | [Bug] Cannot use experiment pattern when using overrides in main config file
# ๐ Bug
When using any override in main config, e.g. for color logging or sweeper:
```yaml
defaults:
- override hydra/hydra_logging: colorlog
- override hydra/job_logging: colorlog
```
Then the experiment configs can't be loa... | diff --git a/hydra/_internal/defaults_list.py b/hydra/_internal/defaults_list.py
--- a/hydra/_internal/defaults_list.py
+++ b/hydra/_internal/defaults_list.py
@@ -464,7 +464,14 @@ def _create_defaults_tree_impl(
self_added = _validate_self(containing_node=parent, defaults=defaults_list)
if is_root_confi... |
facebookresearch__hydra-1487 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hydra/_internal/instantiate/_instantiate2.py:_call_target",
"hydra/_internal/instantiate/_instantiate2.py:instantiate"
],
"edited_modules": [
"hydra/_internal/instantiate/_in... | facebookresearch/hydra | 56cb6d636201b9e832bdc90b72a45202172099df | [Bug] PyTorch Lightning crashes run when optimizer is instatiated with Hydra (dev version)
# ๐ Bug
Hi, should bugs related to hydra dev version be reported? If so I have a couple of interesting edge cases. Here comes the first one.
When instantiating optimizer with Hydra using PyTorch Lightning, using "betas" para... | diff --git a/hydra/_internal/instantiate/_instantiate2.py b/hydra/_internal/instantiate/_instantiate2.py
--- a/hydra/_internal/instantiate/_instantiate2.py
+++ b/hydra/_internal/instantiate/_instantiate2.py
@@ -49,6 +49,16 @@ def _call_target(target: Callable, *args, **kwargs) -> Any: # type: ignore
"""Call targe... |
facebookresearch__hydra-1824 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hydra/_internal/config_loader_impl.py:ConfigLoaderImpl._compose_config_from_defaults_list"
],
"edited_modules": [
"hydra/_internal/config_loader_impl.py:ConfigLoaderImpl"
]
... | facebookresearch/hydra | 7435e573988da956c5df79d9810483955892be73 | Improve error message for merging from defaults list
When composing a config from a defaults list, merge errors can occur if the source config (the selected default) does not fit the schema of the target.
When such an error happens, it would be nice if the error message would say **which** entry in the defaults list... | diff --git a/hydra/_internal/config_loader_impl.py b/hydra/_internal/config_loader_impl.py
--- a/hydra/_internal/config_loader_impl.py
+++ b/hydra/_internal/config_loader_impl.py
@@ -13,7 +13,6 @@
ConfigAttributeError,
ConfigKeyError,
OmegaConfBaseException,
- ValidationError,
)
from hydra._intern... |
facebookresearch__hydra-734 | [
{
"changes": {
"added_entities": [
"hydra/_internal/config_loader_impl.py:ConfigLoaderImpl.split_by_override_type"
],
"added_modules": null,
"edited_entities": [
"hydra/_internal/config_loader_impl.py:ConfigLoaderImpl.split_overrides",
"hydra/_internal/config_load... | facebookresearch/hydra | 8c51854a7d87c25aa1f5e0dccb9bf621639a8dcd | Command line interpolations are not being evaluated lazily, leading to changed multirun behaviour
In v0.11, when I wanted to do multirun with certain parameters dependent on each other, I would do something like
```
./train.py param1=1,2,3 param2=\${param1} -m
```
and this would launch 3 jobs, with same values for ... | diff --git a/hydra/_internal/config_loader_impl.py b/hydra/_internal/config_loader_impl.py
--- a/hydra/_internal/config_loader_impl.py
+++ b/hydra/_internal/config_loader_impl.py
@@ -82,7 +82,7 @@ def __init__(
config_search_path=config_search_path
)
- def split_overrides(
+ def split_by_o... |
facebookresearch__hydra-1488 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tools/configen/configen/configen.py:generate_module"
],
"edited_modules": [
"tools/configen/configen/configen.py:generate_module"
]
},
"file": "tools/configen/configen/... | facebookresearch/hydra | d217c86b9061bb502d00fa971b3ea15a70e3299b | [Bug] [configen] configen fails on modules with `from __future__ import annotations` (default in python 3.10)
# ๐ Bug
## Description
This is the same issue as in omry/omegaconf#303 for which I provided a fix in omry/omegaconf#424. The behavior that will become default in python 3.10, and which can be activated since... | diff --git a/tools/configen/configen/configen.py b/tools/configen/configen/configen.py
--- a/tools/configen/configen/configen.py
+++ b/tools/configen/configen/configen.py
@@ -9,7 +9,7 @@
# Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved
from textwrap import dedent
-from typing import Any, Dict,... |
facebookresearch__hydra-1569 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hydra/_internal/config_loader_impl.py:ConfigLoaderImpl.compute_defaults_list"
],
"edited_modules": [
"hydra/_internal/config_loader_impl.py:ConfigLoaderImpl"
]
},
"file... | facebookresearch/hydra | 321ae22dd751cac976b9f84ce19b6d0144ad5d5f | [Bug] Additional config search paths are not included when using --info defaults commands
# ๐ Bug
## Description
When running hydra apps with additional paths added to the hydra search paths and the command line option `--info defaults` or `--info` is used it seems the additional config search paths are not included... | diff --git a/hydra/_internal/config_loader_impl.py b/hydra/_internal/config_loader_impl.py
--- a/hydra/_internal/config_loader_impl.py
+++ b/hydra/_internal/config_loader_impl.py
@@ -525,11 +525,13 @@ def compute_defaults_list(
run_mode: RunMode,
) -> DefaultsList:
parser = OverridesParser.create... |
facebookresearch__hydra-876 | [
{
"changes": {
"added_entities": [
"hydra/_internal/utils.py:_run_hydra"
],
"added_modules": [
"hydra/_internal/utils.py:_run_hydra"
],
"edited_entities": [
"hydra/_internal/utils.py:run_and_report",
"hydra/_internal/utils.py:run_hydra",
"hyd... | facebookresearch/hydra | 600974f32f096474495d39ed376bbb3a99ddf99a | Add support for specifying an additional config dir in the command line
This is useful for standalone apps that want to come with their own configs but also allow users to add additional configs that can be used with the composition.
```
โโโ my_app.py
โโโ conf
โย ย โโโ config.yaml
โย ย โโโ dataset
โย ย โโโ image... | diff --git a/hydra/_internal/utils.py b/hydra/_internal/utils.py
--- a/hydra/_internal/utils.py
+++ b/hydra/_internal/utils.py
@@ -26,13 +26,9 @@
from omegaconf.errors import OmegaConfBaseException
from hydra._internal.config_search_path_impl import ConfigSearchPathImpl
-from hydra.core.config_search_path import Co... |
facebookresearch__hydra-1458 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hydra/_internal/config_loader_impl.py:ConfigLoaderImpl._load_configuration_impl"
],
"edited_modules": [
"hydra/_internal/config_loader_impl.py:ConfigLoaderImpl"
]
},
"f... | facebookresearch/hydra | 3b5aa5d7d7e98acce42f29dbd8d70cdb4ccf30ec | CLI override of hydra/conf does not require `+` prefix
Not sure if this is a bug or a feature request.
Normally adding a new key using CLI override requires a `+` prefix:
```bash
$ python my_app.py new_key=new_value
Could not override 'new_key'.
To append to your config use +new_key=new_value
Key 'new_key' is n... | diff --git a/hydra/_internal/config_loader_impl.py b/hydra/_internal/config_loader_impl.py
--- a/hydra/_internal/config_loader_impl.py
+++ b/hydra/_internal/config_loader_impl.py
@@ -1,5 +1,4 @@
# Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved
-
import copy
import os
import re
@@ -215,6 +214,8... |
facebookresearch__hydra-1265 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hydra/core/default_element.py:InputDefault.set_package_header"
],
"edited_modules": [
"hydra/core/default_element.py:InputDefault"
]
},
"file": "hydra/core/default_elem... | facebookresearch/hydra | 797c1ed8a554434b4823b534983bdc630ace562c | Changes in package header in Hydra 1.1
- [ ] Deprecate the use cases requiring changes in 1.1
- [ ] Create an upgrade page in the website based on this content.
| diff --git a/hydra/core/default_element.py b/hydra/core/default_element.py
--- a/hydra/core/default_element.py
+++ b/hydra/core/default_element.py
@@ -112,12 +112,25 @@ def is_deleted(self) -> bool:
def set_package_header(self, package_header: Optional[str]) -> None:
assert self.__dict__["package_header... |
facebookresearch__hydra-1661 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"hydra/conf/__init__.py:HydraConf"
]
},
"file": "hydra/conf/__init__.py"
}
] | facebookresearch/hydra | 76f1d799720a0209313afc2faac270d50a415165 | Double printed config
Hey everybody,
I have the problem that each log message is printed out twice. Once with the module name and once with HYDRA (see example output):
```
[2021-06-08 08:14:54,738][HYDRA] config initialized
[2021-06-08 08:14:54,738][soundmap.util.config][INFO] - config initialized
[2021-06-08 ... | diff --git a/hydra/conf/__init__.py b/hydra/conf/__init__.py
--- a/hydra/conf/__init__.py
+++ b/hydra/conf/__init__.py
@@ -125,9 +125,9 @@ class HydraConf:
# Multi-run output configuration
sweep: SweepDir = SweepDir()
# Logging configuration for Hydra
- hydra_logging: Any = MISSING
+ hydra_logging:... |
bokeh__bokeh-13641 | [
{
"changes": {
"added_entities": [
"src/bokeh/models/widgets/tables.py:DataTable.from_data"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"src/bokeh/models/widgets/tables.py:DataTable"
]
},
"file": "src/bokeh/models/widgets/tab... | bokeh/bokeh | 443e3b4c7da50a8cd9e7640f8fa140c84294b655 | [FEATURE] DataTable from_dataframe()
### Problem description
Lack of easy way to create simple tables from pandas DataFrames, with some basic colouring or formatting options
### Feature description
Add a from_dataframe() method to the DataTable class
### Potential alternatives
A create_datatable_from_dataframe() ... | diff --git a/src/bokeh/models/widgets/tables.py b/src/bokeh/models/widgets/tables.py
--- a/src/bokeh/models/widgets/tables.py
+++ b/src/bokeh/models/widgets/tables.py
@@ -45,6 +45,7 @@
Required,
String,
)
+from ...core.property.singletons import Intrinsic
from ...model import Model
from ..sources import CD... |
bokeh__bokeh-13298 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/core/property/container.py:Dict.validate"
],
"edited_modules": [
"src/bokeh/core/property/container.py:Dict"
]
},
"file": "src/bokeh/core/property/container.p... | bokeh/bokeh | 38d05d037223234aedeb25e35502abf3332bf0b4 | Non-specific error when the DataFrame Used to construct a ColumnDataSource contains non-string keys
### Software versions
Python version : 3.9.7 | packaged by conda-forge | (default, Sep 29 2021, 19:20:46)
IPython version : 8.14.0
Tornado version : 6.3.2
Bokeh version : 3.2.1
BokehJS static ... | diff --git a/src/bokeh/core/property/container.py b/src/bokeh/core/property/container.py
--- a/src/bokeh/core/property/container.py
+++ b/src/bokeh/core/property/container.py
@@ -202,11 +202,25 @@ def validate(self, value: Any, detail: bool = True) -> None:
key_is_valid = self.keys_type.is_valid
val... |
bokeh__bokeh-13239 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/core/property/wrappers.py:PropertyValueColumnData._stream"
],
"edited_modules": [
"src/bokeh/core/property/wrappers.py:PropertyValueColumnData"
]
},
"file": "... | bokeh/bokeh | 06a6bf5d7544500431d0fa106c9fec50f15436bf | [BUG] `PropertyValueColumnData._stream()` doesn't handle the case when `rollover` is `0`
### Software versions
Bokeh version: `branch-3.3`
### Expected behavior
If `rollover` is set to 0, calling the `_stream` method within `PropertyValueColumnData` should remove all rows. This behavior can be used to delete ... | diff --git a/src/bokeh/core/property/wrappers.py b/src/bokeh/core/property/wrappers.py
--- a/src/bokeh/core/property/wrappers.py
+++ b/src/bokeh/core/property/wrappers.py
@@ -467,18 +467,18 @@ def _stream(self, doc: Document, source: ColumnarDataSource, new_data: dict[str,
# For arrays is reports the actual ol... |
bokeh__bokeh-13721 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/core/validation/check.py:check_integrity"
],
"edited_modules": [
"src/bokeh/core/validation/check.py:ValidationIssue",
"src/bokeh/core/validation/check.py:Validatio... | bokeh/bokeh | 17b0187a7efac45b27be081aa80416938da3f899 | Errors related to MIN_PREFERRED_MAX_WIDTH while building the docs
Since the merge of #13625 there are quite a few errors in the logs for the documentation build. The source of the warnings below is https://github.com/bokeh/bokeh/actions/runs/7714515006/job/21027112370?pr=13625
```
reading sources... [ 62%] docs/fi... | diff --git a/src/bokeh/core/validation/check.py b/src/bokeh/core/validation/check.py
--- a/src/bokeh/core/validation/check.py
+++ b/src/bokeh/core/validation/check.py
@@ -32,7 +32,7 @@
# Bokeh imports
from ...model import Model
from ...settings import settings
-from ...util.dataclasses import dataclass
+from ...util... |
bokeh__bokeh-13370 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/layouts.py:gridplot"
],
"edited_modules": [
"src/bokeh/layouts.py:gridplot"
]
},
"file": "src/bokeh/layouts.py"
}
] | bokeh/bokeh | cc36ac1df71d7df858560c2182ae2c9c148c846d | [BUG] gridplot got multiple values for keyword argument 'logo'
### Software versions
Python version : 3.9.13 (v3.9.13:6de2ca5339, May 17 2022, 11:23:25)
IPython version : 8.15.0
Tornado version : 6.3.3
Bokeh version : 3.2.2
BokehJS static path : ../lib/python3.9/site-packages/bokeh/server/... | diff --git a/src/bokeh/layouts.py b/src/bokeh/layouts.py
--- a/src/bokeh/layouts.py
+++ b/src/bokeh/layouts.py
@@ -29,6 +29,7 @@
Callable,
Iterable,
Iterator,
+ Literal,
Sequence,
TypeVar,
Union,
@@ -75,6 +76,9 @@
'Spacer',
)
+if TYPE_CHECKING:
+ ToolbarOptions = Literal["log... |
bokeh__bokeh-13535 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "docs/bokeh/source/docs/first_steps/examples/first_steps_2_add_bars.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
... | bokeh/bokeh | 59c2d44928910a03535e82547d4acd4dcd02e71f | [BUG] Unexpected attribute 'size' to Circle
### Software versions
Python version : 3.10.12 | packaged by conda-forge | (main, Jun 23 2023, 22:40:32) [GCC 12.3.0]
IPython version : 8.17.2
Tornado version : 6.3.3
Bokeh version : 3.4.0.dev3+12.g8265814f
BokehJS static path : /home/... | diff --git a/docs/bokeh/source/docs/first_steps/examples/first_steps_2_add_bars.py b/docs/bokeh/source/docs/first_steps/examples/first_steps_2_add_bars.py
--- a/docs/bokeh/source/docs/first_steps/examples/first_steps_2_add_bars.py
+++ b/docs/bokeh/source/docs/first_steps/examples/first_steps_2_add_bars.py
@@ -12,7 +12,... |
bokeh__bokeh-13636 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/embed/elements.py:html_page_for_render_items"
],
"edited_modules": [
"src/bokeh/embed/elements.py:html_page_for_render_items"
]
},
"file": "src/bokeh/embed/el... | bokeh/bokeh | f821f2c549c9541583d8714bc33fac21f3b34588 | Use globally unique and CSS safe IDs in `<script type="application/json">`
### Problem description
Embedding **multiple** Bokeh-html-files with javascript on **one single html-page**, I run into problems.
Reason: Bokeh repeatedly prints this into html-files:
`<script type="application/json" id="p1050"> `
Ho... | diff --git a/src/bokeh/embed/elements.py b/src/bokeh/embed/elements.py
--- a/src/bokeh/embed/elements.py
+++ b/src/bokeh/embed/elements.py
@@ -39,7 +39,7 @@
)
from ..document.document import DEFAULT_TITLE
from ..settings import settings
-from ..util.serialization import make_id
+from ..util.serialization import make... |
bokeh__bokeh-12779 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"examples/server/app/clustering/main.py:clustering"
],
"edited_modules": [
"examples/server/app/clustering/main.py:clustering"
]
},
"file": "examples/server/app/clusteri... | bokeh/bokeh | 0da7e85d29e529c2e5278d5021cc75ecbf4b0d3c | [BUG] ResourceWarning: unclosed file
### Software versions
Python version : 3.10.8 (tags/v3.10.8:aaaf517, Oct 11 2022, 16:50:30) [MSC v.1933 64 bit (AMD64)]
IPython version : 8.10.0
Tornado version : 6.2
Bokeh version : 3.0.3
BokehJS static path : .venv\lib\site-packages\bokeh\server\stat... | diff --git a/examples/server/app/clustering/main.py b/examples/server/app/clustering/main.py
--- a/examples/server/app/clustering/main.py
+++ b/examples/server/app/clustering/main.py
@@ -38,7 +38,7 @@ def clustering(X, algorithm, n_clusters):
# Generate the new colors:
if algorithm=='MiniBatchKMeans':
- ... |
bokeh__bokeh-13041 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/embed/bundle.py:bundle_for_objs_and_resources",
"src/bokeh/embed/bundle.py:_bundle_extensions"
],
"edited_modules": [
"src/bokeh/embed/bundle.py:bundle_for_objs_and... | bokeh/bokeh | 865dda806b83dd04498e61f4f3478569dfaa4687 | [BUG] Domain is not resolved correctly when using BOKEH_RESOURCES=server
### Software versions
# Name Version Build Channel
bokeh 3.0.0.dev16 py_0 bokeh/label/dev
### Browser name and version
_No response_
### Jupyter notebook / Jupyter La... | diff --git a/src/bokeh/embed/bundle.py b/src/bokeh/embed/bundle.py
--- a/src/bokeh/embed/bundle.py
+++ b/src/bokeh/embed/bundle.py
@@ -32,6 +32,7 @@
join,
normpath,
)
+from pathlib import Path
from typing import (
TYPE_CHECKING,
Callable,
@@ -44,10 +45,9 @@
from ..core.templates import CSS_RESOUR... |
bokeh__bokeh-13328 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/core/serialization.py:Serializer._encode_other"
],
"edited_modules": [
"src/bokeh/core/serialization.py:Serializer"
]
},
"file": "src/bokeh/core/serialization... | bokeh/bokeh | 44e140b7b632e1e446c25a231382a05f6045ff46 | Unable to plot a polars.Series with bokeh 3
### Software versions
Python version : 3.11.3 (main, May 4 2023, 15:26:00) [GCC 8.3.0]
IPython version : 8.14.0
Tornado version : 6.3.2
Bokeh version : 3.1.1
BokehJS static path : /home/artem/Study/PyData2023/polars/.venv/lib/python3.11/site-pa... | diff --git a/src/bokeh/core/serialization.py b/src/bokeh/core/serialization.py
--- a/src/bokeh/core/serialization.py
+++ b/src/bokeh/core/serialization.py
@@ -462,6 +462,10 @@ def _encode_other(self, obj: Any) -> AnyRep:
elif obj is pd.NA:
return None
+ # handle array libraries th... |
bokeh__bokeh-12841 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/core/serialization.py:Serializer._encode_other"
],
"edited_modules": [
"src/bokeh/core/serialization.py:Serializer"
]
},
"file": "src/bokeh/core/serialization... | bokeh/bokeh | 78dc3e238194302b5daadf11d47bdd69bd07a2b8 | [BUG] Cannot plot `pandas.DataFrame` with columns of type string
### Software versions
Python: 3.10.2
pandas: 1.5.3
bokeh: 3.0.3
### Browser name and version
Chrome 109.0.5414.119๏ผOfficial Build๏ผ
### Jupyter notebook / Jupyter Lab version
_No response_
### Expected behavior
I want to use toolti... | diff --git a/src/bokeh/core/serialization.py b/src/bokeh/core/serialization.py
--- a/src/bokeh/core/serialization.py
+++ b/src/bokeh/core/serialization.py
@@ -452,8 +452,7 @@ def _encode_other(self, obj: Any) -> AnyRep:
module = type(obj).__module__
if module is not None and module.startswith("pandas"... |
bokeh__bokeh-13404 | [
{
"changes": {
"added_entities": [
"src/bokeh/io/notebook.py:_remote_jupyter_proxy_url",
"src/bokeh/io/notebook.py:_update_notebook_url_from_env"
],
"added_modules": [
"src/bokeh/io/notebook.py:_remote_jupyter_proxy_url",
"src/bokeh/io/notebook.py:_update_notebo... | bokeh/bokeh | 7eaa973b2f61739db84798b0ad533fc15ebcc8ca | [FEATURE] Transparent use on JupyterHub
### Problem description
While it is possible to write Bokeh code to work successfully behind the JupyterHub proxy, it has two drawbacks:
1. Users need to find and learn the work around.
2. A notebook running on a Hub needs code changes so the same notebook will not run ... | diff --git a/src/bokeh/io/notebook.py b/src/bokeh/io/notebook.py
--- a/src/bokeh/io/notebook.py
+++ b/src/bokeh/io/notebook.py
@@ -22,6 +22,8 @@
# Standard library imports
import json
+import os
+import urllib
from typing import (
TYPE_CHECKING,
Any,
@@ -29,6 +31,7 @@
Literal,
Protocol,
Ty... |
bokeh__bokeh-13391 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/server/tornado.py:BokehTornado.resources"
],
"edited_modules": [
"src/bokeh/server/tornado.py:BokehTornado"
]
},
"file": "src/bokeh/server/tornado.py"
}
] | bokeh/bokeh | 0bdaa42ce135a88d1476809fe0439b111c8167c7 | [BUG] Static paths loaded always from localhost in Bokeh 3.1.1
### Software versions
Python version : 3.11.3 (tags/v3.11.3:f3909b8, Apr 4 2023, 23:49:59) [MSC v.1934 64 bit (AMD64)]
IPython version : (not installed)
Tornado version ... | diff --git a/src/bokeh/server/tornado.py b/src/bokeh/server/tornado.py
--- a/src/bokeh/server/tornado.py
+++ b/src/bokeh/server/tornado.py
@@ -605,20 +605,28 @@ def session_token_expiration(self) -> int:
'''
return self._session_token_expiration
- def resources(self, absolute_url: str | None = No... |
bokeh__bokeh-13258 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/core/property/visual.py:Image.transform"
],
"edited_modules": [
"src/bokeh/core/property/visual.py:Image"
]
},
"file": "src/bokeh/core/property/visual.py"
}... | bokeh/bokeh | 3348f65bb545a16523942cbb751ea7384556c53b | [BUG] FileNotFoundError when setting icon for BoxSelectTool
### Software versions
Python version : 3.10.0 (default, Feb 18 2022, 14:12:41) [Clang 12.0.5 (clang-1205.0.22.11)]
IPython version : 8.1.1
Tornado version : 6.3.2
Bokeh version : 3.2.0
BokehJS static path : /Users/oluwafemi.sule/... | diff --git a/src/bokeh/core/property/visual.py b/src/bokeh/core/property/visual.py
--- a/src/bokeh/core/property/visual.py
+++ b/src/bokeh/core/property/visual.py
@@ -24,15 +24,15 @@
import base64
import datetime # lgtm [py/import-and-import-from]
import re
+import tempfile
from io import BytesIO
from pathlib imp... |
bokeh__bokeh-12902 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/embed/util.py:standalone_docs_json_and_render_items"
],
"edited_modules": [
"src/bokeh/embed/util.py:standalone_docs_json_and_render_items"
]
},
"file": "src/... | bokeh/bokeh | 00fd457ddb08027915d25a2fed7368bbbae95807 | `load_notebook()` uses non-unique DOM element IDs
In jupyter lab this can result in autoload nb code not being able to update "BokehJS is loading ..." in the current tab, because it updates it in a different one. This makes it look like bokehjs failed to load.
| diff --git a/src/bokeh/embed/util.py b/src/bokeh/embed/util.py
--- a/src/bokeh/embed/util.py
+++ b/src/bokeh/embed/util.py
@@ -38,7 +38,7 @@
from ..settings import settings
from ..themes.theme import Theme
from ..util.dataclasses import dataclass, field
-from ..util.serialization import make_globally_unique_id
+from... |
bokeh__bokeh-13608 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/embed/bundle.py:bundle_for_objs_and_resources",
"src/bokeh/embed/bundle.py:_query_extensions",
"src/bokeh/embed/bundle.py:_bundle_extensions",
"src/bokeh/embed/bundle.p... | bokeh/bokeh | 824fed30877ccae93a664c59a1ffc434aa848952 | [BUG] Multiple inline math elements in different axes causing axis labels to disappear
### Software versions
Python version : 3.11.6 | packaged by conda-forge | (main, Oct 3 2023, 10:37:07) [Clang 15.0.7 ]
IPython version : (not installed)
Tornado version : 6.3.2
Bokeh version : 3.... | diff --git a/src/bokeh/embed/bundle.py b/src/bokeh/embed/bundle.py
--- a/src/bokeh/embed/bundle.py
+++ b/src/bokeh/embed/bundle.py
@@ -37,13 +37,13 @@
from urllib.parse import urljoin
# Bokeh imports
+from ..core.has_props import HasProps
from ..core.templates import CSS_RESOURCES, JS_RESOURCES
from ..document.do... |
bokeh__bokeh-13198 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/model/util.py:visit_value_and_its_immediate_references"
],
"edited_modules": [
"src/bokeh/model/util.py:visit_value_and_its_immediate_references"
]
},
"file":... | bokeh/bokeh | 47e69a5288727fbfc7b04cb72b32c78bd298536c | [BUG] select(CategoricalColorMapper) returns an empty array
### Software versions
Python version : 3.8.16 | packaged by conda-forge | (default, Feb 1 2023, 16:01:55)
IPython version : 8.11.0
Tornado version : 6.2
Bokeh version : 3.1.0
BokehJS static path : /home/[user]/git/chartify/.con... | diff --git a/src/bokeh/model/util.py b/src/bokeh/model/util.py
--- a/src/bokeh/model/util.py
+++ b/src/bokeh/model/util.py
@@ -25,6 +25,7 @@
# Bokeh imports
from ..core.has_props import HasProps, Qualified
+from ..util.dataclasses import entries, is_dataclass
if TYPE_CHECKING:
from ..core.types import ID
@@... |
bokeh__bokeh-13147 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/models/widgets/sliders.py:DateSlider.value_as_datetime",
"src/bokeh/models/widgets/sliders.py:DateSlider.value_as_date",
"src/bokeh/models/widgets/sliders.py:DateRangeSlider.va... | bokeh/bokeh | 969079b8d319074023a6f28a7374d7f36ff1516a | Replace utcnow and utcfromtimestamp function calls
`datetime.utcnow` and `utcfromtimestamp` will be deprecated in Python 3.12. We use both in our codebase and should replace them, see https://github.com/python/cpython/issues/103857.
| diff --git a/src/bokeh/models/widgets/sliders.py b/src/bokeh/models/widgets/sliders.py
--- a/src/bokeh/models/widgets/sliders.py
+++ b/src/bokeh/models/widgets/sliders.py
@@ -22,7 +22,7 @@
# Standard library imports
import numbers
-from datetime import date, datetime
+from datetime import date, datetime, timezone
... |
bokeh__bokeh-13443 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/core/has_props.py:HasProps.clone"
],
"edited_modules": [
"src/bokeh/core/has_props.py:HasProps"
]
},
"file": "src/bokeh/core/has_props.py"
},
{
"chang... | bokeh/bokeh | b0a59ca015568d8b6229cdb7ddb1508e4c7f504b | Unable to clone models with readonly properties
```py
In [1]: from bokeh.models import *
In [2]: source = ColumnDataSource()
In [3]: source.clone()
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
Cell In[3]... | diff --git a/src/bokeh/core/has_props.py b/src/bokeh/core/has_props.py
--- a/src/bokeh/core/has_props.py
+++ b/src/bokeh/core/has_props.py
@@ -50,6 +50,9 @@ def lru_cache(arg: int | None) -> Callable[[F], F]: ...
else:
from functools import lru_cache
+if TYPE_CHECKING:
+ from typing_extensions import Self
+
... |
bokeh__bokeh-13491 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"examples/plotting/airports_map.py:plot"
],
"edited_modules": [
"examples/plotting/airports_map.py:plot"
]
},
"file": "examples/plotting/airports_map.py"
},
{
"c... | bokeh/bokeh | 6ae71c61f856696297b195125f225fa2e8766efb | `Stamen` tiles were removed from xyzservices 2023.10.1
From https://github.com/geopandas/xyzservices/releases/tag/2023.10.1:
> Stamen tiles have been removed due to their upstream deprecation. Use Stamen styles of Stadia
CI is failing with:
```
tests/test_examples.py::test_file_examples[/home/runner/work/bokeh... | diff --git a/examples/plotting/airports_map.py b/examples/plotting/airports_map.py
--- a/examples/plotting/airports_map.py
+++ b/examples/plotting/airports_map.py
@@ -10,14 +10,13 @@
'''
from bokeh.layouts import column, gridplot
-from bokeh.models import Div, Range1d, WMTSTileSource
+from bokeh.models import Div, ... |
bokeh__bokeh-12867 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/core/serialization.py:Serializer._encode"
],
"edited_modules": [
"src/bokeh/core/serialization.py:Serializer"
]
},
"file": "src/bokeh/core/serialization.py"
... | bokeh/bokeh | 51aca94a6a4a9f3084e7f1b7924215873a54aa9f | [BUG] ColumnDataSource does not work with NumPy floating-point scalars
### Software versions
Python version : 3.7.7 (tags/v3.7.7:d7c567b08f, Mar 10 2020, 10:41:24) [MSC v.1900 64 bit (AMD64)]
IPython version : 7.30.1
Tornado version : 6.0.3
Bokeh version : 2.4.3
BokehJS static path : c:\pyt... | diff --git a/src/bokeh/core/serialization.py b/src/bokeh/core/serialization.py
--- a/src/bokeh/core/serialization.py
+++ b/src/bokeh/core/serialization.py
@@ -283,7 +283,10 @@ def _encode(self, obj: Any) -> AnyRep:
elif isinstance(obj, TypedArray):
return self._encode_typed_array(obj)
eli... |
bokeh__bokeh-13422 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/command/subcommands/info.py:Info.invoke"
],
"edited_modules": [
"src/bokeh/command/subcommands/info.py:Info"
]
},
"file": "src/bokeh/command/subcommands/info.... | bokeh/bokeh | cf57b9ae0073ecf0434a8c10002a70f6bf2079cd | bokeh info should report jupyter_bokeh version if installed
Currently have to actively solicit this information in bug reports, having `bokeh info` report it would save some back and forth.
The module to update is here:
https://github.com/bokeh/bokeh/blob/branch-3.3/src/bokeh/command/subcommands/info.py
And ... | diff --git a/src/bokeh/command/subcommands/info.py b/src/bokeh/command/subcommands/info.py
--- a/src/bokeh/command/subcommands/info.py
+++ b/src/bokeh/command/subcommands/info.py
@@ -17,14 +17,15 @@
.. code-block:: none
- Python version : 3.9.7 | packaged by conda-forge | (default, Sep 29 2021, 19:20:46)
... |
bokeh__bokeh-13289 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/models/renderers/glyph_renderer.py:GlyphRenderer.construct_color_bar"
],
"edited_modules": [
"src/bokeh/models/renderers/glyph_renderer.py:GlyphRenderer"
]
},
... | bokeh/bokeh | d5ce3ec088f06bfaeac1e553bb42b4b88c069f58 | [BUG] construct_color_bar does not support ImageStack glyph
### Software versions
Python version : 3.10.11 | packaged by conda-forge | (main, May 10 2023, 19:01:19) [Clang 14.0.6 ]
IPython version : 8.14.0
Tornado version : 6.3.2
Bokeh version : 3.3.0.dev1+21.gd5ce3ec0
BokehJS static path : ... | diff --git a/src/bokeh/models/renderers/glyph_renderer.py b/src/bokeh/models/renderers/glyph_renderer.py
--- a/src/bokeh/models/renderers/glyph_renderer.py
+++ b/src/bokeh/models/renderers/glyph_renderer.py
@@ -193,6 +193,7 @@ def construct_color_bar(self, **kwargs: Any) -> ColorBar:
from ..glyphs import (
... |
bokeh__bokeh-13318 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/core/property/wrappers.py:PropertyValueColumnData._stream"
],
"edited_modules": [
"src/bokeh/core/property/wrappers.py:PropertyValueColumnData"
]
},
"file": "... | bokeh/bokeh | 99310e6e9140cb4f8e0655eaebe6bab156a94d2e | [BUG] CDS stream broken for larger rollover
### Software versions
Python version : 3.9.10 | packaged by conda-forge | (main, Feb 1 2022, 21:27:48)
IPython version : 8.0.1
Tornado version : 6.1
Bokeh version : 3.2.1
BokehJS static path : /Users/bzaitlen/miniconda3/envs/dask-dev/lib/python3.... | diff --git a/src/bokeh/core/property/wrappers.py b/src/bokeh/core/property/wrappers.py
--- a/src/bokeh/core/property/wrappers.py
+++ b/src/bokeh/core/property/wrappers.py
@@ -477,7 +477,7 @@ def _stream(self, doc: Document, source: ColumnarDataSource, new_data: dict[str,
else:
L = self[k]
... |
bokeh__bokeh-13800 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/embed/server.py:server_document",
"src/bokeh/embed/server.py:server_session"
],
"edited_modules": [
"src/bokeh/embed/server.py:server_document",
"src/bokeh/... | bokeh/bokeh | ca55dcb3d7e7c84de42363c860225d40cd864ec3 | [FEATURE] Allow bokeh server embed script to forward credentials
### Problem description
I want to run a [panel](https://panel.holoviz.org/index.html) application behind a [FastAPI](https://fastapi.tiangolo.com/) server, while the FastAPI server handles the authentication. The [panel documentation](https://panel.hol... | diff --git a/src/bokeh/embed/server.py b/src/bokeh/embed/server.py
--- a/src/bokeh/embed/server.py
+++ b/src/bokeh/embed/server.py
@@ -58,7 +58,7 @@
#-----------------------------------------------------------------------------
def server_document(url: str = "default", relative_urls: bool = False, resources: Litera... |
bokeh__bokeh-13757 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/models/layouts.py:HBox._check_repeated_layout_children",
"src/bokeh/models/layouts.py:VBox._check_repeated_layout_children"
],
"edited_modules": [
"src/bokeh/models... | bokeh/bokeh | 11d9580c4b18e6743b0fb31cd757527e3b414237 | VBox is not working in 3.4.0rc1
### Discussed in https://github.com/bokeh/bokeh/discussions/13742
<div type='discussions-op-text'>
<sup>Originally posted by **GillesFa** March 6, 2024</sup>
Hi,
I have install the following bokeh version:
Python version : 3.11.5 | packaged by Anaconda, Inc. | (main, ... | diff --git a/src/bokeh/models/layouts.py b/src/bokeh/models/layouts.py
--- a/src/bokeh/models/layouts.py
+++ b/src/bokeh/models/layouts.py
@@ -430,7 +430,7 @@ def __init__(self, *args, **kwargs) -> None:
@error(REPEATED_LAYOUT_CHILD)
def _check_repeated_layout_children(self):
- children = [ item["chi... |
Project-MONAI__MONAI-3837 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/apps/deepgrow/transforms.py:SpatialCropForegroundd.__init__",
"monai/apps/deepgrow/transforms.py:SpatialCropForegroundd.__call__"
],
"edited_modules": [
"monai/apps/dee... | Project-MONAI/MONAI | 56205f51cb76d6b8586d0bc2df297348320e2b93 | CropForeground pads asymmetric
**Describe the bug**
In `CropForeground`/`CropForegroundd` the user can request a margin around the foreground voxels. However, currently the margin is only correctly padded on the upper side of a dimension.
See:
https://github.com/Project-MONAI/MONAI/blob/c3db337644d9525610d9fab3cf... | diff --git a/monai/apps/deepgrow/transforms.py b/monai/apps/deepgrow/transforms.py
--- a/monai/apps/deepgrow/transforms.py
+++ b/monai/apps/deepgrow/transforms.py
@@ -369,6 +369,9 @@ class SpatialCropForegroundd(MapTransform):
channel_indices: if defined, select foreground only on the specified channels
... |
Project-MONAI__MONAI-7121 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/apps/utils.py:download_url"
],
"edited_modules": [
"monai/apps/utils.py:download_url"
]
},
"file": "monai/apps/utils.py"
},
{
"changes": {
"added_en... | Project-MONAI/MONAI | 4743945a68952d05c8a97b82b1bb75a3ad5dbf71 | download_url doesn't automatically resolve fuzzy url
```
python /home/runner/work/model-zoo/model-zoo/ci/verify_bundle.py -b renalStructures_CECT_segmentation -m min
Cannot retrieve the public link of the file. You may need to change
the permission to 'Anyone with the link', or have had many accesses.
start v... | diff --git a/monai/apps/utils.py b/monai/apps/utils.py
--- a/monai/apps/utils.py
+++ b/monai/apps/utils.py
@@ -203,6 +203,8 @@ def download_url(
if urlparse(url).netloc == "drive.google.com":
if not has_gdown:
raise RuntimeError("To download files from Google Drive, pl... |
Project-MONAI__MONAI-2238 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/utility/dictionary.py:CopyItemsd.__call__"
],
"edited_modules": [
"monai/transforms/utility/dictionary.py:CopyItemsd"
]
},
"file": "monai/transforms/ut... | Project-MONAI/MONAI | fac93503994d21c877cba6844135f1bd9168c061 | CopyItemsd transform saves data into same key
**Describe the bug**
This line of `CopyItemsd` seems not correct:
https://github.com/Project-MONAI/MONAI/blob/dev/monai/transforms/utility/dictionary.py#L740
It saves all the data of keys into the same `new_key`.
| 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
@@ -730,10 +730,11 @@ def __call__(self, data):
"""
d = dict(data)
- for new_key in self.names:
- i... |
Project-MONAI__MONAI-4800 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/utils/deprecate_utils.py:warn_deprecated",
"monai/utils/deprecate_utils.py:deprecated",
"monai/utils/deprecate_utils.py:deprecated_arg"
],
"edited_modules": [
"... | Project-MONAI/MONAI | 288edee10dee580f99c594bdcc4909bd1623c6b5 | flake8-pyi
the issue also happens in `MONAI` repo (https://github.com/Project-MONAI/MONAI/runs/7604721904?check_suite_focus=true#step:7:188), what do you think?
_Originally posted by @yiheng-wang-nv in https://github.com/Project-MONAI/model-zoo/issues/71#issuecomment-1200716404_
deprecated warning with futurewarnin... | diff --git a/monai/utils/deprecate_utils.py b/monai/utils/deprecate_utils.py
--- a/monai/utils/deprecate_utils.py
+++ b/monai/utils/deprecate_utils.py
@@ -27,15 +27,19 @@ class DeprecatedError(Exception):
pass
-def warn_deprecated(obj, msg):
+def warn_deprecated(obj, msg, warning_category=FutureWarning):
... |
Project-MONAI__MONAI-855 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/inferers/utils.py:sliding_window_inference"
],
"edited_modules": [
"monai/inferers/utils.py:sliding_window_inference"
]
},
"file": "monai/inferers/utils.py"
}
] | Project-MONAI/MONAI | ba3d34d5c29dea5a0d19e524ee4176cebb992a71 | sliding_window_inference uses to much gpu memory if roi_size is small and images to infer large
**Describe the bug**
sliding_window_inference runns ot of memory if roi_size is small and images to infer large
**To Reproduce**
evaluete a highres3dnet with images larger than 512x512x256 and roi_size of the sliding_wi... | diff --git a/monai/inferers/utils.py b/monai/inferers/utils.py
--- a/monai/inferers/utils.py
+++ b/monai/inferers/utils.py
@@ -9,7 +9,7 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from typing import Callable, Sequence, Tuple, Union
+from typing import C... |
Project-MONAI__MONAI-2621 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/synthetic.py:create_test_image_2d",
"monai/data/synthetic.py:create_test_image_3d"
],
"edited_modules": [
"monai/data/synthetic.py:create_test_image_2d",
"... | Project-MONAI/MONAI | f943ab4126b37894b3aa5336ceae828731c126d6 | Bugs in `create_test_image_2d` and `create_test_image_3d`
**Describe the bug**
1) There is a limitation in the current implementation:
The following line:
```
rad = rs.randint(5, rad_max)
```
requires `rad_max` be larger than 5.
I think we should not use the magic number `5` here, and there is no docstring... | diff --git a/monai/data/synthetic.py b/monai/data/synthetic.py
--- a/monai/data/synthetic.py
+++ b/monai/data/synthetic.py
@@ -23,23 +23,25 @@ def create_test_image_2d(
height: int,
num_objs: int = 12,
rad_max: int = 30,
+ rad_min: int = 5,
noise_max: float = 0.0,
num_seg_classes: int = 5,
... |
Project-MONAI__MONAI-7548 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"monai/losses/perceptual.py:PercetualNetworkType"
]
},
"file": "monai/losses/perceptual.py"
}
] | Project-MONAI/MONAI | 95f69dea3d2ff9fb3d0695d922213aefaf5f0c39 | Perceptual loss with medicalnet_resnet50_23datasets errors due to a typo.
**Describe the bug**
When trying to use `network_type=medicalnet_resnet50_23datasets`, I got the following error:
```
ValueError: Unrecognised criterion entered for Adversarial Loss. Must be one in: alex, vgg, squeeze, radimagenet_resnet50, me... | diff --git a/monai/losses/perceptual.py b/monai/losses/perceptual.py
--- a/monai/losses/perceptual.py
+++ b/monai/losses/perceptual.py
@@ -29,7 +29,7 @@ class PercetualNetworkType(StrEnum):
squeeze = "squeeze"
radimagenet_resnet50 = "radimagenet_resnet50"
medicalnet_resnet10_23datasets = "medicalnet_resn... |
Project-MONAI__MONAI-4402 | [
{
"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 | 554de62dfe884513af392d858aba5a41e2ef9c13 | improve error message of `get_parsed_content`
**Is your feature request related to a problem? Please describe.**
when the config component can't be instantiated due to typos,
the error message should show some details of the failed component.
currently the message is not straightforward, for example:
```py
from ... | 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
@@ -281,7 +281,10 @@ def instantiate(self, **kwargs) -> object: # type: ignore
modname = self.resolve_module_name()
args = self.resolve_args()
args.updat... |
Project-MONAI__MONAI-2421 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/spatial/array.py:Spacing.__init__",
"monai/transforms/spatial/array.py:Spacing.__call__",
"monai/transforms/spatial/array.py:Orientation.__init__",
"monai/transf... | Project-MONAI/MONAI | 88fe0fc082b25e1830ac53b4d6c20169d4a4175b | Transforms: Spacing output not compatible with CenterScaleCrop
**Describe the bug**
`Spacing` transform also outputs affine information. `CenterScaleCrop` expects a tuple of 1 and not 3. `Spacingd` followed by `CenterScaleCropd` works fine.
**To Reproduce**
```
import numpy as np
from monai.transforms import (Co... | 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
@@ -88,6 +88,7 @@ def __init__(
padding_mode: Union[GridSamplePadMode, str] = GridSamplePadMode.BORDER,
align_corners: bool = False,
... |
Project-MONAI__MONAI-4186 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/decathlon_datalist.py:load_decathlon_datalist"
],
"edited_modules": [
"monai/data/decathlon_datalist.py:load_decathlon_datalist"
]
},
"file": "monai/data/dec... | Project-MONAI/MONAI | 5c15138f484ba027b90fd12f7038a519f740d213 | data list utility enhancement
**Is your feature request related to a problem? Please describe.**
the current data list utility assumes that when the key is `"test"`, the data is a list of filenames. https://github.com/Project-MONAI/MONAI/blob/ed1c281a0f1b0d9c364ed59020a69ab2a821a5f2/monai/data/decathlon_datalist.py#L1... | 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
@@ -122,7 +122,8 @@ def load_decathlon_datalist(
if data_list_key not in json_data:
raise ValueError(f'Data list {data_list_key} not specified in "... |
Project-MONAI__MONAI-3464 | [
{
"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 | 82576e7e37e571a1e7055fdb2193f7b2ff634a6e | `reduction` for `ContrastiveLoss`
**Describe the bug**
the error messages and docstring should be consistent
https://github.com/Project-MONAI/MONAI/blob/a7bc4a3cbaeaa3c505a25ca2ddf6922bda8ea7dc/monai/losses/contrastive.py#L89-L91
https://github.com/Project-MONAI/MONAI/blob/a7bc4a3cbaeaa3c505a25ca2ddf6922bda8ea7dc/... | diff --git a/monai/losses/contrastive.py b/monai/losses/contrastive.py
--- a/monai/losses/contrastive.py
+++ b/monai/losses/contrastive.py
@@ -9,13 +9,11 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from typing import Union
-
import torch
from torch.nn... |
Project-MONAI__MONAI-2214 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/apps/deepgrow/transforms.py:SpatialCropForegroundd.__init__",
"monai/apps/deepgrow/transforms.py:SpatialCropForegroundd.__call__",
"monai/apps/deepgrow/transforms.py:AddGuidanceFro... | Project-MONAI/MONAI | e6258c9f841a72fd78936378036da220b46be698 | Add `meta_key` arg to enhance the `meta_key_postfix` arg
**Is your feature request related to a problem? Please describe.**
Currently, we use `meta_key_postfix` to extract meta data from dict, but sometimes it may not have corresponding meta key for the specified key, like `pred` and `pred_meta_dict`.
So we need an a... | diff --git a/monai/apps/deepgrow/transforms.py b/monai/apps/deepgrow/transforms.py
--- a/monai/apps/deepgrow/transforms.py
+++ b/monai/apps/deepgrow/transforms.py
@@ -18,7 +18,7 @@
from monai.transforms import Resize, SpatialCrop
from monai.transforms.transform import MapTransform, Randomizable, Transform
from monai... |
Project-MONAI__MONAI-6429 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "monai/transforms/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/t... | Project-MONAI/MONAI | 7ea082e2d38d0e6028dc3fb3cb04796e05528d3f | spatial resample -- adaptive padding mode when switching the backends
for the array pad functions there's numpy->torch mode str adaptation
https://github.com/Project-MONAI/MONAI/blob/554b172d2b173ea1bacba34e2ff32e80b261da20/monai/transforms/croppad/functional.py#L41-L43
would be great to implement the same idea for... | diff --git a/monai/transforms/__init__.py b/monai/transforms/__init__.py
--- a/monai/transforms/__init__.py
+++ b/monai/transforms/__init__.py
@@ -660,6 +660,7 @@
rescale_instance_array,
reset_ops_id,
resize_center,
+ resolves_modes,
sync_meta_info,
weighted_patch_samples,
zero_margins,... |
Project-MONAI__MONAI-6034 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/inferers/utils.py:sliding_window_inference"
],
"edited_modules": [
"monai/inferers/utils.py:sliding_window_inference"
]
},
"file": "monai/inferers/utils.py"
}
] | Project-MONAI/MONAI | 88fb0b10d85f59e9ee04cbeeddb28b91f2ea209b | `sliding_window_inference` shouldn't remove gradient
**Describe the bug**
```py
import torch
import monai
inputs = torch.ones((3, 16, 15, 7), requires_grad=True)
result = monai.inferers.sliding_window_inference(inputs, roi_size=(2, 3), sw_batch_size=3, predictor=lambda x: x + 1.0)
result.sum().backward()
print... | diff --git a/monai/inferers/utils.py b/monai/inferers/utils.py
--- a/monai/inferers/utils.py
+++ b/monai/inferers/utils.py
@@ -262,7 +262,7 @@ def sliding_window_inference(
# account for any overlapping sections
for ss in range(len(output_image_list)):
- output_image_list[ss] = output_image_list[ss].... |
Project-MONAI__MONAI-2576 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/nifti_saver.py:NiftiSaver.__init__",
"monai/data/nifti_saver.py:NiftiSaver.save"
],
"edited_modules": [
"monai/data/nifti_saver.py:NiftiSaver"
]
},
"... | Project-MONAI/MONAI | f420d9962fa8d6de281c4066221d8459ef6a7610 | Save segmentation results in the same folder
**Is your feature request related to a problem? Please describe.**
Feature requested in discussion: https://github.com/Project-MONAI/MONAI/discussions/2069#discussioncomment-978827.
@jnc13:
Since it is a related question to this discussion, is there a way to avoid having ... | 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
@@ -47,6 +47,7 @@ def __init__(
output_dtype: DtypeLike = np.float32,
squeeze_end_dims: bool = True,
data_root_dir: str = "",
+ separate_folder: bool = Tru... |
Project-MONAI__MONAI-5526 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/utility/dictionary.py:Lambdad.__init__",
"monai/transforms/utility/dictionary.py:Lambdad.__call__"
],
"edited_modules": [
"monai/transforms/utility/dictionar... | Project-MONAI/MONAI | 8ac7df4e36448c6884198a9e02194f4cfb8a3f0b | Transforms enhancement for HoVerNet
In the original HoVerNet repo(https://github.com/vqdang/hover_net), they use imgaug(https://github.com/aleju/imgaug) to do data augmentation, which has several differences with MONAI.
- [x] add `new_key` in `Lambda` (addressed by #5526)
Now in `Lambdad`, if we set overwri... | 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
@@ -1032,8 +1032,10 @@ class Lambdad(MapTransform, InvertibleTransform):
each element corresponds to a key in ``keys``.
... |
Project-MONAI__MONAI-3340 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "monai/apps/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/apps/ut... | Project-MONAI/MONAI | e148cfdb0b0ad90db2cc247e6d27cb5124d30cdb | unit test error from `python -m tests.clang_format_utils`
**Describe the bug**
error from `python -m tests.clang_format_utils`
```
2021-11-14 22:26:15,861 - INFO - Downloaded: /__w/MONAI/MONAI/.clang-format-bin/clang-format
2021-11-14 22:26:15,864 - ERROR - check_hash failed 938869fb71b05f5ba345ab36dfbbc4388f53a550... | diff --git a/monai/apps/__init__.py b/monai/apps/__init__.py
--- a/monai/apps/__init__.py
+++ b/monai/apps/__init__.py
@@ -11,4 +11,4 @@
from .datasets import CrossValidation, DecathlonDataset, MedNISTDataset
from .mmars import MODEL_DESC, RemoteMMARKeys, download_mmar, get_model_spec, load_from_mmar
-from .utils i... |
Project-MONAI__MONAI-5965 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/handlers/stats_handler.py:StatsHandler.__init__",
"monai/handlers/stats_handler.py:StatsHandler.attach"
],
"edited_modules": [
"monai/handlers/stats_handler.py:StatsHan... | Project-MONAI/MONAI | 5657b8f2d297e2d2b09017cf9f57dad2a72186f4 | overriding iteration_log and epoch_log in StatsHandler
Currently, they are booleans but we could extend them to `Union[bool, Callable]` where if arg is callable then it could be used for event filtering:
```python
def attach(self, engine):
if self.iteration_log and not engine.has_event_handler(sel... | diff --git a/monai/handlers/stats_handler.py b/monai/handlers/stats_handler.py
--- a/monai/handlers/stats_handler.py
+++ b/monai/handlers/stats_handler.py
@@ -66,8 +66,8 @@ class StatsHandler:
def __init__(
self,
- iteration_log: bool = True,
- epoch_log: bool = True,
+ iteration_lo... |
Project-MONAI__MONAI-7180 | [
{
"changes": {
"added_entities": [
"monai/data/grid_dataset.py:GridPatchDataset.set_data",
"monai/data/grid_dataset.py:GridPatchDataset._fill_cache",
"monai/data/grid_dataset.py:GridPatchDataset._load_cache_item",
"monai/data/grid_dataset.py:GridPatchDataset._generate_patch... | Project-MONAI/MONAI | a3064eb1e5323adff56d7198497e9ed22b5606a5 | Patch dataset seems extremely inefficient in training
Hello! Thank you for this incredible library! I'm loving my experience with MONAI so far.
**Is your feature request related to a problem? Please describe.**
But I've noticed a severe inefficiency in the way PatchDataset is written. If used with RandSpacialCropSamp... | diff --git a/monai/data/grid_dataset.py b/monai/data/grid_dataset.py
--- a/monai/data/grid_dataset.py
+++ b/monai/data/grid_dataset.py
@@ -11,18 +11,30 @@
from __future__ import annotations
-from collections.abc import Callable, Generator, Hashable, Iterable, Mapping, Sequence
+import sys
+import warnings
+from co... |
Project-MONAI__MONAI-7754 | [
{
"changes": {
"added_entities": [
"docs/source/conf.py:linkcode_resolve"
],
"added_modules": [
"docs/source/conf.py:linkcode_resolve"
],
"edited_entities": null,
"edited_modules": null
},
"file": "docs/source/conf.py"
},
{
"changes": {
"... | Project-MONAI/MONAI | a052c4435a088a1e87f2d41279822109edbd59fd | matplotlib 3.9.0 has no attribute 'get_cmap
**Describe the bug**
Hi, when I ran some [checks](https://github.com/Project-MONAI/MONAI/actions/runs/9110117156/job/25044447504?pr=7712) before merging (#7712 ), there were some bugs.
Because of the [check](https://github.com/Project-MONAI/MONAI/actions/runs/9095604464/job... | diff --git a/docs/source/conf.py b/docs/source/conf.py
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -13,6 +13,8 @@
import os
import subprocess
import sys
+import importlib
+import inspect
sys.path.insert(0, os.path.abspath(".."))
sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__)... |
Project-MONAI__MONAI-4688 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/utils.py:collate_meta_tensor"
],
"edited_modules": [
"monai/data/utils.py:collate_meta_tensor"
]
},
"file": "monai/data/utils.py"
}
] | Project-MONAI/MONAI | 3b12a2403286b8681d9a98ea97c5a47c0ec9c742 | collate_meta_tensor can't work with `ImageDataset`
**Describe the bug**
Thanks for @KumoLiu 's issue report, when using MetaTensor with `ImageDataset`, the decollate raised error:
```
File "unet_training_array.py", line 167, in <module>
main(tempdir)
File "unet_training_array.py", line 137, in main
va... | diff --git a/monai/data/utils.py b/monai/data/utils.py
--- a/monai/data/utils.py
+++ b/monai/data/utils.py
@@ -433,6 +433,9 @@ def collate_meta_tensor(batch):
return collated
if isinstance(elem_0, Mapping):
return {k: collate_meta_tensor([d[k] for d in batch]) for k in elem_0}
+ if isinstance(... |
Project-MONAI__MONAI-2530 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/apps/deepgrow/interaction.py:Interaction.__call__"
],
"edited_modules": [
"monai/apps/deepgrow/interaction.py:Interaction"
]
},
"file": "monai/apps/deepgrow/inter... | Project-MONAI/MONAI | 17dde67bbf95991b6c7465724e41653d22972449 | Deepgrow `Interaction` is not compatiable with `decollate_batch` for v 0.6.0 (8/July)
**Describe the bug**
In deepgrow tutorial (https://github.com/Project-MONAI/tutorials/blob/master/deepgrow/ignite/train.py#L201), we can see there are two groups of transforms: `pre_transforms` and `click_transforms`, and `click_tran... | diff --git a/monai/apps/deepgrow/interaction.py b/monai/apps/deepgrow/interaction.py
--- a/monai/apps/deepgrow/interaction.py
+++ b/monai/apps/deepgrow/interaction.py
@@ -12,6 +12,7 @@
import torch
+from monai.data import decollate_batch, list_data_collate
from monai.engines import SupervisedEvaluator, Supervised... |
Project-MONAI__MONAI-3715 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/engines/evaluator.py:Evaluator.__init__"
],
"edited_modules": [
"monai/engines/evaluator.py:Evaluator"
]
},
"file": "monai/engines/evaluator.py"
}
] | Project-MONAI/MONAI | d36b835b226ab95ffae5780629a5304d8df5883e | `mode` of Evaluator can't work with string input
**Describe the bug**
Issue reported by @holgerroth :
this is for the saliency map inference. I need to run the evaluation in "training mode". SupervisedEvaluator in monai has that option but I guess it doesn't support the `str` type. it's checking for ForwardMode.EVAL... | diff --git a/monai/engines/evaluator.py b/monai/engines/evaluator.py
--- a/monai/engines/evaluator.py
+++ b/monai/engines/evaluator.py
@@ -114,7 +114,7 @@ def __init__(
event_to_attr=event_to_attr,
decollate=decollate,
)
- self.mode = look_up_option(mode, ForwardMode)
+ ... |
Project-MONAI__MONAI-5405 | [
{
"changes": {
"added_entities": [
"monai/networks/nets/hovernet.py:HoVerNet.freeze_encoder",
"monai/networks/nets/hovernet.py:_load_pretrained_encoder"
],
"added_modules": [
"monai/networks/nets/hovernet.py:_load_pretrained_encoder"
],
"edited_entities": [
... | Project-MONAI/MONAI | 3f1eac82c5a17520a49b93d557df3fd7ef9304ec | Inconsistent places of HoverNet
When I compared our implementation of HoverNet and the [referred version](https://github.com/vqdang/hover_net/blob/master/models/hovernet/net_desc.py), I found a different place:
for each residual block, the kernel size of the second conv layer is 3 (see [here](https://github.com/vqdang... | diff --git a/monai/networks/nets/hovernet.py b/monai/networks/nets/hovernet.py
--- a/monai/networks/nets/hovernet.py
+++ b/monai/networks/nets/hovernet.py
@@ -27,12 +27,16 @@
# }
# =========================================================================
+import os
+import re
+import warnings
from collections impo... |
Project-MONAI__MONAI-3208 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/engines/workflow.py:Workflow._register_metrics"
],
"edited_modules": [
"monai/engines/workflow.py:Workflow"
]
},
"file": "monai/engines/workflow.py"
},
{
... | Project-MONAI/MONAI | cc136c009a0620e73c53d341bfad6d9d448d7a6a | Add different reductions in metric handlers
**Is your feature request related to a problem? Please describe.**
Currently, all the metric handlers set `reduction=MEAN`.
It would be nice to add reduction support for metric handlers, and if the metric is key metric to compare, must use "MEAN" reduction.
| diff --git a/monai/engines/workflow.py b/monai/engines/workflow.py
--- a/monai/engines/workflow.py
+++ b/monai/engines/workflow.py
@@ -20,7 +20,7 @@
from monai.config import IgniteInfo
from monai.engines.utils import IterationEvents, default_metric_cmp_fn, default_prepare_batch
from monai.transforms import Decollate... |
Project-MONAI__MONAI-2061 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/handlers/iteration_metric.py:IterationMetric.update"
],
"edited_modules": [
"monai/handlers/iteration_metric.py:IterationMetric"
]
},
"file": "monai/handlers/iter... | Project-MONAI/MONAI | 13bf996409eb04b2fddf753f6aedb2a4b71ccec3 | Add support to compute metrics on list of images and tensor label
**Is your feature request related to a problem? Please describe.**
Need to support the case that the image is a list of tensors and label is only 1 tensor during metrics computation.
| 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
@@ -80,8 +80,8 @@ def _compute(y_pred, y):
score = self.metric_fn(y_pred, y)
return score[0] if isinstance(score, (tuple, list)... |
Project-MONAI__MONAI-4044 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/handlers/utils.py:write_metrics_reports"
],
"edited_modules": [
"monai/handlers/utils.py:write_metrics_reports"
]
},
"file": "monai/handlers/utils.py"
}
] | Project-MONAI/MONAI | 167a3206c9007d367cffc4a2a667ea4da2e10e37 | cannot import name 'PILLOW_VERSION' from 'PIL'
The issue is found when trying to fix #4011 , and it is raised due to `torchvision==0.2.2` is installed (the version is too old).
conda test TestHandlerMetricsSaver
**Describe the bug**
```
======================================================================
FAIL: tes... | diff --git a/monai/handlers/utils.py b/monai/handlers/utils.py
--- a/monai/handlers/utils.py
+++ b/monai/handlers/utils.py
@@ -121,7 +121,10 @@ class mean median max 5percentile 95percentile notnans
with open(os.path.join(save_dir, f"{k}_raw.csv"), "w") as f:
f.write(f"filenam... |
Project-MONAI__MONAI-4796 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/handlers/probability_maps.py:ProbMapProducer.__call__"
],
"edited_modules": [
"monai/handlers/probability_maps.py:ProbMapProducer"
]
},
"file": "monai/handlers/pr... | Project-MONAI/MONAI | c1eaf427ed2310483856e33e57e7b83d59c85b13 | ProbMap indexing has an error
**Describe the bug**
The location values of probability mask is not being used correctly in the numpy output. The locations are a numpy array (instead of a tuple) so when used in indexing an ndarray, they are not being interpreted as the location in two/three dimension. Instead they are t... | diff --git a/monai/handlers/probability_maps.py b/monai/handlers/probability_maps.py
--- a/monai/handlers/probability_maps.py
+++ b/monai/handlers/probability_maps.py
@@ -95,7 +95,7 @@ def __call__(self, engine: Engine) -> None:
locs = engine.state.batch["metadata"][ProbMapKeys.LOCATION]
probs = engin... |
Project-MONAI__MONAI-3882 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/image_writer.py:NibabelWriter.write"
],
"edited_modules": [
"monai/data/image_writer.py:NibabelWriter"
]
},
"file": "monai/data/image_writer.py"
}
] | Project-MONAI/MONAI | 775935da263f55f8269bb5a42676d18cba4b9a08 | inconsistent output s/qform code for SaveImage
**Describe the bug**
```py
import numpy as np
import nibabel as nib
from monai.transforms import SaveImaged, LoadImaged
from monai.data import ITKWriter, NibabelWriter
# create a testing volume
img = nib.Nifti1Image(np.ones((3, 4, 5, 1, 1)), np.eye(4))
img.header... | 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
@@ -601,6 +601,12 @@ def write(self, filename: PathLike, verbose: bool = False, **obj_kwargs):
self.data_obj = self.create_backend_obj(
self.data_obj, affine=self.... |
Project-MONAI__MONAI-2325 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/io/array.py:switch_endianness",
"monai/transforms/io/array.py:LoadImage.__call__"
],
"edited_modules": [
"monai/transforms/io/array.py:switch_endianness",
... | Project-MONAI/MONAI | 89ee6af11f313307335ed164c756ae522bedf519 | 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/transforms/io/array.py b/monai/transforms/io/array.py
--- a/monai/transforms/io/array.py
+++ b/monai/transforms/io/array.py
@@ -13,6 +13,7 @@
https://github.com/Project-MONAI/MONAI/wiki/MONAI_Design
"""
+import sys
from typing import Dict, List, Optional, Sequence, Union
import numpy as np
@@... |
Project-MONAI__MONAI-4344 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"monai/utils/enums.py:InterpolateMode"
]
},
"file": "monai/utils/enums.py"
}
] | Project-MONAI/MONAI | eb60b9caf0a103af53ab5f3d620ceb2c116a4851 | InterpolateMode add support for 'nearest-exact' mode
**Is your feature request related to a problem? Please describe.**
There's a bug of 'nearest' mode of torch.nn.functional.interpolate in pytorch. This may lead mismatch between 'nearest' and other mode.
Plese see:
[https://github.com/pytorch/pytorch/pull/64501... | 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
@@ -264,7 +264,7 @@ class ZoomBoxd(MapTransform, InvertibleTransform):
zoom: The zoom factor along t... |
Project-MONAI__MONAI-3186 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"monai/transforms/intensity/array.py:MaskIntensity"
]
},
"file": "monai/transforms/intensity/array.py"
},
{
"changes": {
"added_entities": null,
... | Project-MONAI/MONAI | e5ddf2026b27f8c34923b09f4c8e78606eb8d773 | Some transforms randomly output numpy or tensor that can't collate
**Describe the bug**
Thanks for @rijobro 's reminder https://github.com/Project-MONAI/MONAI/pull/3113#discussion_r727913518, I double checked the transforms today and found we truly have such issue in several transforms:
https://github.com/Project-MO... | 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
@@ -941,7 +941,7 @@ class MaskIntensity(Transform):
"""
- backend = [TransformBackends.NUMPY]
+ backend = [TransformBackends.TORCH, Tr... |
Project-MONAI__MONAI-6008 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/image_reader.py:PILReader.__init__",
"monai/data/image_reader.py:PILReader.get_data"
],
"edited_modules": [
"monai/data/image_reader.py:PILReader"
]
},
... | Project-MONAI/MONAI | f4902b220538f02f3621b37c3e1f2067c830e0fe | option for LoadImage to be compatible with torchvision save_image
**Is your feature request related to a problem? Please describe.**
for 2d natural images the current loader is not consistent with the common computer vision conversion:
```py
import numpy as np
import torchvision
import monai
from monai.transfor... | 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
@@ -1141,13 +1141,17 @@ class PILReader(ImageReader):
Args:
converter: additional function to convert the image data after `read()`.
for example, use `convert... |
Project-MONAI__MONAI-1836 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/spatial/array.py:AffineGrid.__call__",
"monai/transforms/spatial/array.py:AffineGrid.get_transformation_matrix",
"monai/transforms/spatial/array.py:RandAffineGrid.__call... | Project-MONAI/MONAI | b6d1cea9a864aad527d7bcc7aa9669b19370cadc | AffineGrid GPU tensor error
**Describe the bug**
a transform error from `AffineGrid` when running tutorial `transforms_demo_2d`
full logs: https://github.com/Project-MONAI/MONAI/runs/2172199805?check_suite_focus=true
```
Running ./modules/transforms_demo_2d.ipynb
Checking PEP8 compliance...
Running notebook...
... | 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
@@ -961,7 +961,7 @@ def __call__(
self,
spatial_size: Optional[Sequence[int]] = None,
grid: Optional[Union[np.ndarray, torch.Tenso... |
Project-MONAI__MONAI-2482 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "monai/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/utils/deprec... | Project-MONAI/MONAI | 2085a49820be146ad953ece23041540a237e08b6 | enhance the version comparison utililty
**Is your feature request related to a problem? Please describe.**
version comparison is needed for a few cases:
- https://github.com/Project-MONAI/MONAI/blob/2085a49820be146ad953ece23041540a237e08b6/tests/utils.py#L133-L136
- https://github.com/Project-MONAI/MONAI/blob/2085a4... | diff --git a/monai/__init__.py b/monai/__init__.py
--- a/monai/__init__.py
+++ b/monai/__init__.py
@@ -18,8 +18,8 @@
PY_REQUIRED_MINOR = 6
version_dict = get_versions()
-__version__ = version_dict.get("version", "0+unknown")
-__revision_id__ = version_dict.get("full-revisionid")
+__version__: str = version_dict.get... |
Project-MONAI__MONAI-5416 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/losses/dice.py:DiceCELoss.forward",
"monai/losses/dice.py:DiceFocalLoss.__init__",
"monai/losses/dice.py:DiceFocalLoss.forward"
],
"edited_modules": [
"monai/lo... | Project-MONAI/MONAI | 8925e3eea656dd1c24c90db70449c44d8ca0f044 | include_background=False, softmax=True doesn't work properly in DiceFocalLoss for binary segmentation
**Environment**
monai 1.0.1
**Describe the bug**
When using `include_background=False, softmax=True` in DiceFocalLoss for binary segmentation, the Dice part produces this warning and does not apply softmax when ca... | diff --git a/monai/losses/dice.py b/monai/losses/dice.py
--- a/monai/losses/dice.py
+++ b/monai/losses/dice.py
@@ -60,12 +60,12 @@ def __init__(
include_background: if False, channel index 0 (background category) is excluded from the calculation.
if the non-background segmentations are sma... |
Project-MONAI__MONAI-3636 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/grid_dataset.py:GridPatchDataset.__init__",
"monai/data/grid_dataset.py:GridPatchDataset.__iter__",
"monai/data/grid_dataset.py:PatchDataset.__init__"
],
"edited_m... | Project-MONAI/MONAI | 83f8b06372a3803ebe9281300cb794a1f3395018 | Enhance GridPatchDataset for iterable dataset
**Is your feature request related to a problem? Please describe.**
Meng zhang and I are preparing examples for MONAI webinar to show all kinds of MONAI datasets, realized that the `GridPatchDataset` can be enhanced as we already have the `IterableDataset` now and we can ea... | diff --git a/monai/data/grid_dataset.py b/monai/data/grid_dataset.py
--- a/monai/data/grid_dataset.py
+++ b/monai/data/grid_dataset.py
@@ -9,16 +9,13 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from typing import Callable, Dict, Optional, Sequence, Unio... |
Project-MONAI__MONAI-4843 | [
{
"changes": {
"added_entities": [
"monai/data/meta_tensor.py:MetaTensor.__str__"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"monai/data/meta_tensor.py:MetaTensor"
]
},
"file": "monai/data/meta_tensor.py"
}
] | Project-MONAI/MONAI | 38bc8fad9fcfa1078b69308c9e32b4da8ff2b1cc | MetaTensor Needs `__str__` Method
**Is your feature request related to a problem? Please describe.**
When a `MetaTensor` is printed with `print` it produces its metadata information in addition to what a tensor would normally print. This is usually too verbose for just printing to screen, and differs from default beha... | 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
@@ -503,4 +503,16 @@ def ensure_torch_and_prune_meta(
return MetaTensor(img, meta=meta)
def __repr__(self, *, tensor_contents=None):
+ """
+ Prints out a long ... |
Project-MONAI__MONAI-2952 | [
{
"changes": {
"added_entities": [
"monai/transforms/utility/dictionary.py:DeleteItemsd.__init__"
],
"added_modules": null,
"edited_entities": [
"monai/transforms/utility/dictionary.py:DeleteItemsd.__call__"
],
"edited_modules": [
"monai/transforms/uti... | Project-MONAI/MONAI | ff9c80fb4fc62cb17b6880a8a5d9f7f07e53bb14 | 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/transforms/utility/dictionary.py b/monai/transforms/utility/dictionary.py
--- a/monai/transforms/utility/dictionary.py
+++ b/monai/transforms/utility/dictionary.py
@@ -17,6 +17,7 @@
import copy
import logging
+import re
from copy import deepcopy
from typing import Any, Callable, Dict, Hashable,... |
Project-MONAI__MONAI-4638 | [
{
"changes": {
"added_entities": [
"monai/data/meta_tensor.py:MetaTensor.astype"
],
"added_modules": null,
"edited_entities": [
"monai/data/meta_tensor.py:MetaTensor.ensure_torch_and_prune_meta"
],
"edited_modules": [
"monai/data/meta_tensor.py:MetaTen... | Project-MONAI/MONAI | 4ddd2bc3870a86fb0a300c20e680de48886bbfc1 | convert_to_numpy issue
**Describe the bug**
```py
>>> from monai.utils import convert_to_numpy
>>> import torch
>>> import numpy as np
>>> convert_to_numpy(data=torch.zeros((2,2),dtype=torch.long), dtype=np.uint16)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "monai/utils/type... | 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
@@ -15,13 +15,15 @@
from copy import deepcopy
from typing import Any, Sequence
+import numpy as np
import torch
from monai.config.type_definitions import NdarrayTensor
from monai.d... |
Project-MONAI__MONAI-6385 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/utility/array.py:Lambda.__init__",
"monai/transforms/utility/array.py:Lambda.__call__",
"monai/transforms/utility/array.py:RandLambda.__init__",
"monai/transform... | Project-MONAI/MONAI | e18097d0a8ba323ee66aeb7830d296bf54f44bdd | Lambda transform should allow type conversion based on user-defined function
**Is your feature request related to a problem? Please describe.**
In the current implementation of Lambda transform, it always forces a conversion to MetaTensor when the output type is a numpy.ndarray or torch.Tensor and metadata tracking is... | 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
@@ -830,6 +830,8 @@ class Lambda(InvertibleTransform):
Args:
func: Lambda/function to be applied.
inv_func: Lambda/function of inverse... |
Project-MONAI__MONAI-3923 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/networks/nets/unetr.py:UNETR.proj_feat",
"monai/networks/nets/unetr.py:UNETR.forward",
"monai/networks/nets/unetr.py:UNETR.__init__"
],
"edited_modules": [
"mon... | Project-MONAI/MONAI | c319ca8ff31aa980a045f1b913fb2eb22aadb080 | network UNETR does not support torchscript
May need to add the support for it.
| diff --git a/monai/networks/nets/unetr.py b/monai/networks/nets/unetr.py
--- a/monai/networks/nets/unetr.py
+++ b/monai/networks/nets/unetr.py
@@ -179,24 +179,25 @@ def __init__(
res_block=res_block,
)
self.out = UnetOutBlock(spatial_dims=spatial_dims, in_channels=feature_size, out_channe... |
Project-MONAI__MONAI-3378 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/apps/pathology/transforms/spatial/array.py:SplitOnGrid.__call__",
"monai/apps/pathology/transforms/spatial/array.py:TileOnGrid.__call__"
],
"edited_modules": [
"monai/a... | Project-MONAI/MONAI | 37930a9bc433ae3faf11e762550362cb8a241c43 | Add `numpy` support to `SplitOnGrid`
**Is your feature request related to a problem? Please describe.**
`SplitOnGrid` transform for digital pathology only supports `torch.Tensor` backend, it would be nice to have the `numpy` backend implementation as well.
Discussed at https://github.com/Project-MONAI/MONAI/issues/... | 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
@@ -15,7 +15,9 @@
import torch
from numpy.lib.stride_tricks import as_strided
+from monai.con... |
Project-MONAI__MONAI-1884 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/utility/dictionary.py:ConcatItemsd.__init__"
],
"edited_modules": [
"monai/transforms/utility/dictionary.py:ConcatItemsd"
]
},
"file": "monai/transform... | Project-MONAI/MONAI | 76beeb224731e145fe0891aac0fe02e486203ec4 | allows for single key in `ConcatItemsd`
Hi everyone I'm using `ConcatItemsd` for concatenating the inputs from multi-modalities images. During development sometimes I adjust the number of modalities of inputs, even to single modality. However I found that `ConcatItemsd` in monai currently does not allow this, with an ... | 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
@@ -675,8 +675,6 @@ def __init__(self, keys: KeysCollection, name: str, dim: int = 0, allow_missing_
"""
super().__in... |
Project-MONAI__MONAI-1684 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/networks/nets/densenet.py:_load_state_dict"
],
"edited_modules": [
"monai/networks/nets/densenet.py:_load_state_dict"
]
},
"file": "monai/networks/nets/densenet.p... | Project-MONAI/MONAI | 7cfb52970f5b4a2ddfdf81a2d517e1d5ca90309a | Densenet pretrained weights issue
**Describe the bug**
In #1259 , some layer names of Densenet have changed, thus these layers cannot load weights (trained in ImageNet, provided by Pytorch Hub) correctly.
I'll submit a PR to fix this issue, and add the consistency test case to prevent the same issues in the future.
| 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
@@ -210,14 +210,14 @@ def _load_state_dict(model, model_url, progress):
<https://github.com/pytorch/vision/blob/master/torchvision/models/densenet.py>`_
""... |
Project-MONAI__MONAI-4251 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/wsi_datasets.py:PatchWSIDataset._transform"
],
"edited_modules": [
"monai/data/wsi_datasets.py:PatchWSIDataset"
]
},
"file": "monai/data/wsi_datasets.py"
}... | Project-MONAI/MONAI | 812275ae5f4a1bc8a69b70a9823632b6f30a5724 | Split WSI regions into sub-patches without new dimension
**Is your feature request related to a problem? Please describe.**
`GridSplit` stack up all the split patches in a new dimension, which makes sense; however, for some use cases like the classification-based pathology tumor detection, we want to treat each of the... | diff --git a/monai/data/wsi_datasets.py b/monai/data/wsi_datasets.py
--- a/monai/data/wsi_datasets.py
+++ b/monai/data/wsi_datasets.py
@@ -127,11 +127,13 @@ def _get_data(self, sample: Dict):
def _transform(self, index: int):
# Get a single entry of data
sample: Dict = self.data[index]
+
... |
Project-MONAI__MONAI-5183 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/intensity/array.py:ComputeHoVerMaps.__call__"
],
"edited_modules": [
"monai/transforms/intensity/array.py:ComputeHoVerMaps"
]
},
"file": "monai/transfo... | Project-MONAI/MONAI | b36ba6c84f8f56c08e80b16acace9d466b70078a | Inconsistent dim in `ComputeHoVerMaps`
**Is your feature request related to a problem? Please describe.**
In `ComputeHoVerMaps`, the input shape is (H[, W, D]) which may be inconsistent with most other transforms that need channel dimension.
https://github.com/Project-MONAI/MONAI/blob/9689abf834f004f49ca59c7fe931caf2... | 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
@@ -2293,6 +2293,7 @@ def __call__(self, image: NdarrayOrTensor):
class ComputeHoVerMaps(Transform):
"""Compute horizontal and vertical maps fr... |
Project-MONAI__MONAI-6514 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/wsi_reader.py:CuCIMWSIReader._get_patch",
"monai/data/wsi_reader.py:TiffFileWSIReader._get_patch"
],
"edited_modules": [
"monai/data/wsi_reader.py:CuCIMWSIReader",... | Project-MONAI/MONAI | 7f3d3fc79e0caa0953f801c903368e74a65a8773 | Bug for changing `channel_dim` in Whole slide image reader
I tried to change the default value for `channel_dim` in `CuCIMWSIReader` and found that the outputs were not correct. Therefore, I checked the source code and identified the buggy part:
https://github.com/Project-MONAI/MONAI/blob/e5cf74aac60cb3512d92f9abb3dd4... | diff --git a/monai/data/wsi_reader.py b/monai/data/wsi_reader.py
--- a/monai/data/wsi_reader.py
+++ b/monai/data/wsi_reader.py
@@ -824,7 +824,7 @@ def _get_patch(
f"The image is expected to have three or four color channels in '{mode}' mode but has "
f"{patch.shape[self.channel... |
Project-MONAI__MONAI-1030 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/image_reader.py:ImageReader.read",
"monai/data/image_reader.py:ImageReader.get_data",
"monai/data/image_reader.py:ITKReader.__init__",
"monai/data/image_reader.py:ITKR... | Project-MONAI/MONAI | 1a4175047966a45cf9dd4ae1cef539ef46300f6d | ImageReader can't support multi-threads
**Describe the bug**
As we have some member variables in the ImageReaders, it can't support multi-threads so far, need to update it.
PyTorch DataLoader is multi-processing, so we didn't realize this issue before.
| 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
@@ -54,23 +54,27 @@ def verify_suffix(self, filename: Union[Sequence[str], str]) -> bool:
raise NotImplementedError(f"Subclass {self.__class__.__name__} must implement this met... |
Project-MONAI__MONAI-2096 | [
{
"changes": {
"added_entities": [
"monai/handlers/classification_saver.py:ClassificationSaver._started",
"monai/handlers/classification_saver.py:ClassificationSaver._finalize"
],
"added_modules": null,
"edited_entities": [
"monai/handlers/classification_saver.py:... | Project-MONAI/MONAI | 5eb919869b4211b8f8146a89132127c5fb6bec89 | ClassificationSaver can't work if ranks have different iterations
**Describe the bug**
Currently, if the ranks have different iteration number, it will hang when it try to `all_gather` info from ranks.
| diff --git a/monai/handlers/classification_saver.py b/monai/handlers/classification_saver.py
--- a/monai/handlers/classification_saver.py
+++ b/monai/handlers/classification_saver.py
@@ -10,12 +10,15 @@
# limitations under the License.
import logging
-from typing import TYPE_CHECKING, Callable, Optional
+import war... |
Project-MONAI__MONAI-6912 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/spatial/dictionary.py:Spacingd.__call__"
],
"edited_modules": [
"monai/transforms/spatial/dictionary.py:Spacingd"
]
},
"file": "monai/transforms/spatia... | Project-MONAI/MONAI | 2862f53a7f755641dd375198260ea68484e69a95 | Spacingd changes the output shape unexpectedly
**Describe the bug**
Assume I have three images A, B and C, which I want to transform using one Spacingd instance.
Images A and B already have the desired target pixdim, I thus expect the application of Spacingd to not have an effect. Image C does not have the desired... | diff --git a/monai/transforms/spatial/dictionary.py b/monai/transforms/spatial/dictionary.py
--- a/monai/transforms/spatial/dictionary.py
+++ b/monai/transforms/spatial/dictionary.py
@@ -517,7 +517,8 @@ def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = No
output_spatial_shap... |
Project-MONAI__MONAI-7318 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/io/array.py:SaveImage.__init__",
"monai/transforms/io/array.py:SaveImage.__call__"
],
"edited_modules": [
"monai/transforms/io/array.py:SaveImage"
]
... | Project-MONAI/MONAI | b1c8b42d03bf3c1daabd6c39a35fcbdadb57e8b0 | Support specified filenames in `Saveimage`
Now `SaveImage` only supports specified the `output_name_formatter` which makes it a little complicated for users.
https://github.com/Project-MONAI/MONAI/blob/b1c8b42d03bf3c1daabd6c39a35fcbdadb57e8b0/monai/transforms/io/array.py#L393C14-L393C14
Add support specified `filen... | diff --git a/monai/transforms/io/array.py b/monai/transforms/io/array.py
--- a/monai/transforms/io/array.py
+++ b/monai/transforms/io/array.py
@@ -414,6 +414,9 @@ def __init__(
self.fname_formatter = output_name_formatter
self.output_ext = output_ext.lower() or output_format.lower()
+ sel... |
Project-MONAI__MONAI-5845 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/meta_tensor.py:MetaTensor.update_meta"
],
"edited_modules": [
"monai/data/meta_tensor.py:MetaTensor"
]
},
"file": "monai/data/meta_tensor.py"
}
] | Project-MONAI/MONAI | 4b464e7b6bee1b52fa0be4d72a4662f384f095af | Slicing a MetaTensor: `TypeError: only integer tensors of a single element can be converted to an index`
The goal is to slice the tensor in half. For some reason that I cannot comprehend, it doesn't work on a particular tensor:
```python
>>> type(x)
<class 'monai.data.meta_tensor.MetaTensor'>
>>> x.shape
torch... | 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
@@ -235,11 +235,19 @@ def update_meta(rets: Sequence, func, args, kwargs) -> Sequence:
# respectively. Don't need to do anything with the metadata.
... |
Project-MONAI__MONAI-2696 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/transforms/spatial/array.py:Resize.__call__"
],
"edited_modules": [
"monai/transforms/spatial/array.py:Resize"
]
},
"file": "monai/transforms/spatial/array.py"
... | Project-MONAI/MONAI | f6ad4ba5c2a6ecd8ab0ca18da1c20b0112a18d87 | `Resize` error
**Describe the bug**
Resized shape may not equal to the expected shape.
The error come from: https://github.com/Project-MONAI/MONAI/blob/dev/monai/transforms/spatial/array.py#L406
**To Reproduce**
```
from monai.transforms import Resize
resize_transform = Resize(spatial_size=1008, size_mode... | 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
@@ -14,7 +14,6 @@
"""
import warnings
-from math import ceil
from typing import Any, List, Optional, Sequence, Tuple, Union
import numpy as np
@@ -40... |
Project-MONAI__MONAI-3001 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"monai/data/dataset.py:CacheDataset.__init__",
"monai/data/dataset.py:CacheDataset._transform",
"monai/data/dataset.py:SmartCacheDataset.__init__"
],
"edited_modules": [
... | Project-MONAI/MONAI | 790fc8f572322c6a4c1ab527acfb27447be4bb66 | Add support to avoid deepcopy in CacheDataset
**Is your feature request related to a problem? Please describe.**
Currently, we always `deepcopy` the cache content for every epoch in `CacheDataset`, actually it's not necessary for multi-processing DataLoader or the random transforms don't change the cache data at all.
... | diff --git a/monai/data/dataset.py b/monai/data/dataset.py
--- a/monai/data/dataset.py
+++ b/monai/data/dataset.py
@@ -575,6 +575,7 @@ def __init__(
cache_rate: float = 1.0,
num_workers: Optional[int] = None,
progress: bool = True,
+ copy_cache: bool = True,
) -> None:
""... |
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