Commit Graph

119 Commits (039ba5d4ca8ba208dd1195899667d6067330a7bd)

Author SHA1 Message Date
谢昕辰 a947e3e754
[FIx] Set default `backend_args` values to None (#2597)
## Motivation

In MMEngine >= 0.2.0, it might directly determine what the backend is by
using the `data_root` path.

## Modification

Set all default `backend_args` values are `None`.
2023-02-16 15:33:52 +08:00
CSH 2e27f8b678
[Enhancement]Replace numpy ascontiguousarray with torch contiguous to speed-up (#2604)
## Motivation

Original motivation was after [MMDetection PR
#9533](https://github.com/open-mmlab/mmdetection/pull/9533)

With several experiments I found out that if a ndarray is contiguous,
numpy.transpose + torch.contiguous perform better, while if not, then
use numpy.ascontiguousarray + numpy.transpose

## Modification

Replace numpy.ascontiguousarray with torch.contiguous in
[PackSegInputs](https://github.com/open-mmlab/mmsegmentation/blob/1.x/mmseg/datasets/transforms/formatting.py)

Co-authored-by: MeowZheng <meowzheng@outlook.com>
2023-02-15 19:02:00 +08:00
Andrew Lau 49b062e365
CodeCamp #139 [Feature] Support REFUGE dataset. (#2554)
## Motivation 
Add REFUGE datasets
Old PR: https://github.com/open-mmlab/mmsegmentation/pull/2420

---------

Co-authored-by: MengzhangLI <mcmong@pku.edu.cn>
2023-02-03 16:02:19 +08:00
谢昕辰 124b87ce90
[Refactor] Refactor fileio (#2543)
## Motivation

Use the new fileio from mmengine
https://github.com/open-mmlab/mmengine/pull/533

## Modification

1. Use `mmengine.fileio` to repalce FileClient  in mmseg/datasets
2. Use `mmengine.fileio` to repalce FileClient in
mmseg/datasets/transforms
3. Use `mmengine.fileio` to repalce FileClient in mmseg/visualization

## BC-breaking (Optional)

we modify all the dataset configurations, so please use the latest config file.
2023-02-01 17:53:22 +08:00
Siddharth Ancha d1c0a3efd4
[Fix] Unfinished label conversion from `-1` to `255` in 1.x (#2516)
## Motivation

This is motivated by a previously unfinished PR (#2332). In that PR, the
label -1 was changed to 255 in `BaseSegDataset`, which is correct.
However, it was changed at only one location. There is another location
in `mmseg/datasets/basesegdataset.py` where -1 was still being used that
was not converted to 255. I have now converted it to 255.

This is exactly same as a similar fix to the `master` branch via #2515 .

## Modification

I've simply converted the snipped

```python
if new_id != -1:
    new_palette.append(palette[old_id])
```
to 
```python
if new_id != 255:
    new_palette.append(palette[old_id])
```

## Checklist

- [x] Pre-commit or other linting tools are used to fix the potential
lint issues.
  - _I've fixed all linting/pre-commit errors._
- [x] The modification is covered by complete unit tests. If not, please
add more unit test to ensure the correctness.
  - _No unit tests need to be added or were affected.
- [x] If the modification has potential influence on downstream
projects, this PR should be tested with downstream projects, like MMDet
or MMDet3D.
  - _I don't think this change affects MMDet or MMDet3D._
- [x] The documentation has been modified accordingly, like docstring or
example tutorials.
- _This change fixes an existing bug and doesn't require modifying any
documentation/docstring._
2023-01-30 12:35:55 +08:00
Siddharth Ancha 74e8b89b17
[Fix] Switch order of `reduce_zero_label` and applying `label_map` in 1.x (#2517)
This is an almost exact duplicate of #2500 (that was made to the
`master` branch) now applied to the `1.x` branch.

---

## Motivation

I want to fix a bug through this PR. The bug occurs when two options --
`reduce_zero_label=True`, and custom classes are used.
`reduce_zero_label` remaps the GT seg labels by remapping the zero-class
to 255 which is ignored. Conceptually, this should occur *before* the
`label_map` is applied, which maps *already reduced labels*. However,
currently, the `label_map` is applied before the zero label is reduced.

## Modification

The modification is simple:
- I've just interchanged the order of the two operations by moving a few
lines from bottom to top.
- I've added a test that passes when the fix is introduced, and fails on
the original `master` branch.

## BC-breaking (Optional)

I do not anticipate this change braking any backward-compatibility.

## Checklist

- [x] Pre-commit or other linting tools are used to fix the potential
lint issues.
  - _I've fixed all linting/pre-commit errors._
- [x] The modification is covered by complete unit tests. If not, please
add more unit test to ensure the correctness.
  - _I've added a unit test._ 
- [x] If the modification has potential influence on downstream
projects, this PR should be tested with downstream projects, like MMDet
or MMDet3D.
  - _I don't think this change affects MMDet or MMDet3D._
- [x] The documentation has been modified accordingly, like docstring or
example tutorials.
- _This change fixes an existing bug and doesn't require modifying any
documentation/docstring._
2023-01-30 12:17:15 +08:00
Leeinsn 7fc8ca0312
CodeCamp #141 [Feature] Add BioMedical3DRandomFlip. (#2404)
## Motivation

Support for biomedical 3d images augmentation.

## Modification

Add BioMedical3DRandomFlip in mmseg/datasets/transforms/transforms.py.

Co-authored-by: MeowZheng <meowzheng@outlook.com>
2023-01-20 15:34:11 +08:00
Vladimir Loginov 6d8ba3b5a0
Update basesegdataset.py (#2492)
## Motivation

Makes docstring to be consistent with actual argument name.

## Modification

Minor fix

## BC-breaking (Optional)

No
2023-01-17 20:18:46 +08:00
Wencheng Wu 8dae9465a6
[Feature] Add `gt_edge_map` field. (#2466)
## Motivation

The motivation of this PR is to add `gt_edge_map` field to support
boundary loss.

## Modification

- GenerateEdge
Modify `gt_edge` field to `gt_edge_map`.

- PackSegInputs
Add `gt_edge_map` to data_sample.

- stack_batch
Pad `gt_edge_map` to max_shape.

## BC-breaking (Optional)

No

## Use cases (Optional)

Reference `GenerateEdge`.
2023-01-11 11:51:29 +08:00
谢昕辰 f90f7a56d4
[Fix] Fix incorrect `img_shape` value assignment in RandomCrop (#2469)
## Motivation

Fix incorrect `img_shape` value assignment.

## Modification

- mmseg/datasets/transforms/transforms.py
2023-01-10 18:03:43 +08:00
王永韬 2d67e51db3
CodeCamp #140 [New] [Feature] Add synapse dataset and data augmentation in dev-1.x. (#2432)
## Motivation

Add Synapse dataset in MMSegmentation.
Old PR: https://github.com/open-mmlab/mmsegmentation/pull/2372.
2023-01-06 16:14:54 +08:00
legendchilli 6af2b8eab9
[Feature] Add BioMedical3DPad (#2383)
## Motivation
Add the 3d pad transform for biomedical images, which follows the design
of the nnUNet.
2023-01-03 13:37:48 +08:00
Fivethousand 3ca690bad3
[Feature] Add BioMedicalRandomGamma (#2406)
Add the random gamma correction transform for biomedical images, which
follows the design of the nnUNet.
2023-01-02 21:29:03 +08:00
Haoyu Wang 26f3df7a45
[Feature] nnUNet-style Gaussian Noise and Blur (#2373)
## Motivation

implement nnUNet-style Gaussian Noise and Blur
2023-01-02 20:43:15 +08:00
Jin Ye 79e8578bfc [Feature] Add Biomedical 3D array random crop transform (#2378)
* [Feature] Add Biomedical 3D array random crop transform

* fix lint

* fix gen crop bbox

* fix gen crop bbox

* docstring

* typo

Co-authored-by: MeowZheng <meowzheng@outlook.com>
2022-12-30 22:52:07 +08:00
Miao Zheng f3db8d779d
[Fix]Add input argument for datasets (#2379) 2022-12-05 22:27:04 +08:00
xiexinch 3b731edbd3 update copyright 2022-12-01 13:58:17 +08:00
xiexinch 5a62b0335f fix h,w order 2022-12-01 11:25:00 +08:00
xiexinch 721afaec31 add docstring 2022-11-24 16:22:07 +08:00
xiexinch 1910dffd6c minor change 2022-11-24 15:02:50 +08:00
xiexinch 68e3b25560 use mmcv.RandomChoiceResize as entry 2022-11-24 14:55:25 +08:00
xiexinch 721f4d01f3 add ut 2022-11-23 15:15:38 +08:00
xiexinch 056edc8e1a init 2022-11-22 19:51:38 +08:00
MengzhangLI cfab5b39c0 [Fix] Fix ignore class id from -1 to 255 in BaseSegDataset in 1.x 2022-11-22 00:52:36 +08:00
MengzhangLI 2d4b113b5d [Fix] Fix typo of BaseSegDataset docstring 2022-11-18 17:20:03 +08:00
Miao Zheng b21df463d4
[Feature] LIP dataset (#2187)
* [WIP] LIP dataset

* wip

* keep473

* lip dataset prepare

* add ut and test data
2022-10-31 20:47:52 +08:00
Miao Zheng 3d8fd35e26
[Feature]Add Decathlon dataset (#2227)
* [Feature]Add Decathlon dataset

* fix test data

* add file

* remove order

* revise default value for prefix

* modify example

* revise based on  comments

* add comments for ut
2022-10-26 20:10:42 +08:00
Miao Zheng ac9ee8c355
[Feature]Generate Edge for dataset (#2210)
* [WIP]Generate Edge for dataset

* add ut

* add repr

* add inti
2022-10-20 16:45:31 +08:00
Miao Zheng 20c7dc689c
[Feature] Add BioMedical data loading (#2176)
* [WIP] Add BioMedical data loading

* add depends nibabel

* fix bug

* fix ut

* fix

* add test data

* xyz2zyx zyx2xyz

* format

* remove ignore empty

* remove ignore empty

* remove with seg in LoadBiomedicalAnnotation

* float32

* docstring

* toxyz

* docstring
2022-10-18 16:30:08 +08:00
MengzhangLI f3cd44bebf
[Fix] Fix ResizeToMultiple transform in MMSeg 1.x (#2185) 2022-10-14 15:37:35 +08:00
Miao Zheng 8de0050f25
[Refactor] data flow (#1956)
* [WIP] Refactor data flow

* model return

* [WIP] Refactor data flow

* support data_samples is optional

* fix benchmark

* fix base

* minors

* rebase

* fix api

* ut

* fix api inference

* comments

* docstring

* docstring

* docstring

* fix bug of slide inference

* add assert c > 1
2022-08-26 15:54:23 +08:00
Miao Zheng 50546da85c
[Fix]Remove modules from mmcv.runner and mmcv.utils (#1966)
* [WIP] mmcv-clean

* [WIP]Remove modules from mmcv.runner and mmcv.utils

* wip

* fix import mmengine

* remove ut

* loadcheckpoint in mae
2022-08-25 15:15:21 +08:00
谢昕辰 3d98c25052 fix base dataset (#1926) 2022-08-19 20:50:03 +08:00
Miao Zheng e0499d5a77 [Fix] Fix repo based on refactoring standard (#1869)
* [Fix] Fix repo based on refactory standard

* fix ut
2022-08-19 20:50:02 +08:00
谢昕辰 167f94a70b rename data to structures (#1854) 2022-08-19 20:50:02 +08:00
MengzhangLI ecab73a892 [Feature] Add P1 DataTransform (#1843)
* [Feature] Add P1 DataTransform

* fix unit test error

* fix @cache_randomness location
2022-08-19 20:50:01 +08:00
MengzhangLI e4b9d72a11
[Fix] 2.0 Fix mDice metric for medical datasets (#1864) 2022-08-04 18:32:52 +08:00
MengzhangLI 3cf2bbda2a
[Fix] Change CustomDataset to BaseSegDataset (#1791) 2022-07-26 12:01:40 +08:00
谢昕辰 ba4d1d62aa
[Feature] Add LoadImageFromNdArray pipeline (#1810)
* add load image from ndarray pipeline

* fix import
2022-07-22 19:40:00 +08:00
Miao Zheng 4de57b49c5
[Fix] Fix register_all_modules and imports (#1793)
* [Fix] Fix register_all_modules and imports

* fix transforms import
2022-07-21 22:44:42 +08:00
zhengmiao 4b76f277a6 [Refactory] MMSegmentation Content 2022-07-15 15:47:29 +00:00
xiexinchen.vendor d74dc89214 [Refactor] Fix load annotations by file 2022-07-11 11:31:38 +00:00
xiexinch 761e1a9983 minor change 2022-07-05 20:43:33 +08:00
zhengmiao 89d6f89dfc Merge branch 'linfangjian/refactor_citysmetric' into 'refactor_dev'
[Refactor] Refactor cityscapes metrics

See merge request openmmlab-enterprise/openmmlab-ce/mmsegmentation!46
2022-06-28 03:21:33 +00:00
linfangjian.vendor 6053345b3d [Refactor] Refactor cityscapes metrics 2022-06-28 03:21:33 +00:00
limengzhang.vendor f2bac79f03 [Refactor] Refactor DatasetWrapper 2022-06-27 14:36:18 +00:00
zhengmiao b23982d1b3 [Refactory] Refactory BaseSegmentor based BaseModel 2022-06-19 06:32:09 +00:00
MengzhangLI 7a78d6e483 [Fix] Fix METAINFO typo in ChaseDB1Dataset 2022-06-09 20:49:32 +08:00
zhengmiao f59ef99b00 [Fix]Add label_map and reduce_zero_label in metainfo of dataset and deprecate reduce_zero_label in load annotation 2022-06-09 12:23:36 +00:00
MengzhangLI c061d6d30e [Fix] Fix omitting to_tensor in PackSegInputs 2022-06-09 11:01:56 +08:00