From ed6ab885c366a2080bd580d451dbed14df4c569e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Wiebke=20K=C3=B6pp?= Date: Tue, 20 Feb 2024 16:45:11 -0800 Subject: [PATCH 1/8] :art: Add pre-commit hooks and Github action for linting and formatting --- .flake8 | 7 +++++++ .github/workflows/test-lint.yml | 34 +++++++++++++++++++++++++++++++++ .pre-commit-config.yaml | 17 +++++++++++++++++ requirements-dev.txt | 11 ++++++----- 4 files changed, 64 insertions(+), 5 deletions(-) create mode 100644 .flake8 create mode 100644 .github/workflows/test-lint.yml create mode 100644 .pre-commit-config.yaml diff --git a/.flake8 b/.flake8 new file mode 100644 index 00000000..77dac34a --- /dev/null +++ b/.flake8 @@ -0,0 +1,7 @@ +[flake8] +# 127 is width of the Github code viewer, +# black default is 88 so this will only warn about comments >127 +max-line-length = 127 +# Ignore errors due to incompatibility with black +#https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html +extend-ignore = E203,E701 \ No newline at end of file diff --git a/.github/workflows/test-lint.yml b/.github/workflows/test-lint.yml new file mode 100644 index 00000000..50bcda28 --- /dev/null +++ b/.github/workflows/test-lint.yml @@ -0,0 +1,34 @@ +name: test-and-lint + +on: pull_request + +jobs: + test-and-lint: + runs-on: ubuntu-22.04 + steps: + - uses: actions/checkout@v3 + with: + fetch-depth: 0 + - name: Set up Python 3.9.16 + uses: actions/setup-python@v3 + with: + python-version: '3.9.16' + - name: Install dependencies + run: | + python -m pip install --upgrade pip + if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi + - name: Lint with flake8 + run: | + # stop the build if there are Python syntax errors or undefined names + flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + - name: Run isort + uses: isort/isort-action@master + - name: Test formatting with black + run: | + black . --check + - name: Run pytest + run: | + python -m pytest \ No newline at end of file diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 00000000..cad41cce --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,17 @@ +default_language_version: + python: python3 +repos: + # Using this mirror lets us use mypyc-compiled black, which is about 2x faster + - repo: https://github.com/psf/black-pre-commit-mirror + rev: 24.2.0 + hooks: + - id: black + - repo: https://github.com/pycqa/flake8 + rev: 7.0.0 + hooks: + - id: flake8 + - repo: https://github.com/pycqa/isort + rev: 5.13.2 + hooks: + - id: isort + args: ["--profile", "black"] diff --git a/requirements-dev.txt b/requirements-dev.txt index c96047ec..e0e86de3 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -1,7 +1,8 @@ -black==22.10.0 -flake8==6.0.0 -tiled[all] +black==24.2.0 +flake8==7.0.0 +tiled[all]==0.1.0a114 pytest pytest-mock -isort==5.12.0 -greenlet==2.0.2 \ No newline at end of file +isort==5.13.2 +greenlet==2.0.2 +pre-commit==3.6.2 From 7502baa5fa1eff0d5270378e9ed5a12a70bf779c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Wiebke=20K=C3=B6pp?= Date: Tue, 20 Feb 2024 16:56:02 -0800 Subject: [PATCH 2/8] Ignore flake8 errors for callback imports and long cmd commands --- app.py | 6 +++--- callbacks/segmentation.py | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/app.py b/app.py index f9eb1e7b..c8514d9d 100644 --- a/app.py +++ b/app.py @@ -4,9 +4,9 @@ import dash_mantine_components as dmc from dash import Dash, dcc -from callbacks.control_bar import * -from callbacks.image_viewer import * -from callbacks.segmentation import * +from callbacks.control_bar import * # noqa: F403, F401 +from callbacks.image_viewer import * # noqa: F403, F401 +from callbacks.segmentation import * # noqa: F403, F401 from components.control_bar import layout as control_bar_layout from components.image_viewer import layout as image_viewer_layout diff --git a/callbacks/segmentation.py b/callbacks/segmentation.py index 3ff288f9..ce425a95 100644 --- a/callbacks/segmentation.py +++ b/callbacks/segmentation.py @@ -24,7 +24,7 @@ "job_kwargs": { "uri": "mlexchange1/random-forest-dc:1.1", "type": "docker", - "cmd": 'python random_forest.py data/seg-results/spiral/image-train data/seg-results-test/spiral/feature data/seg-results/spiral/mask data/seg-results-test/spiral/model \'{"n_estimators": 30, "oob_score": true, "max_depth": 8}\'', + "cmd": 'python random_forest.py data/seg-results/spiral/image-train data/seg-results-test/spiral/feature data/seg-results/spiral/mask data/seg-results-test/spiral/model \'{"n_estimators": 30, "oob_score": true, "max_depth": 8}\'', # noqa: E501 "kwargs": { "job_type": "train", "experiment_id": "123", @@ -41,7 +41,7 @@ "job_kwargs": { "uri": "mlexchange1/random-forest-dc:1.1", "type": "docker", - "cmd": "python segment.py data/data/20221222_085501_looking_from_above_spiralUP_CounterClockwise_endPointAtDoor_0-1000 data/seg-results-test/spiral/model/random-forest.model data/seg-results-test/spiral/output '{\"show_progress\": 1}'", + "cmd": "python segment.py data/data/20221222_085501_looking_from_above_spiralUP_CounterClockwise_endPointAtDoor_0-1000 data/seg-results-test/spiral/model/random-forest.model data/seg-results-test/spiral/output '{\"show_progress\": 1}'", # noqa: E501 "kwargs": { "job_type": "train", "experiment_id": "124", From 8e4bd069e2cd31b819df069157ba370054036c9f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Wiebke=20K=C3=B6pp?= Date: Tue, 20 Feb 2024 17:03:03 -0800 Subject: [PATCH 3/8] Result of `pre-commit run --all-files` and manual flake8 fixes --- callbacks/control_bar.py | 31 ++++++++++++++++++++++++------- callbacks/image_viewer.py | 16 ++++++++-------- callbacks/segmentation.py | 2 -- components/annotation_class.py | 3 ++- components/control_bar.py | 11 ++++++++--- components/image_viewer.py | 1 - utils/annotations.py | 1 - utils/data_utils.py | 28 ++++++++++++++-------------- utils/download_sample_data.py | 3 ++- utils/plot_utils.py | 5 ++--- 10 files changed, 60 insertions(+), 41 deletions(-) diff --git a/callbacks/control_bar.py b/callbacks/control_bar.py index 645185bb..700a7dea 100644 --- a/callbacks/control_bar.py +++ b/callbacks/control_bar.py @@ -58,7 +58,8 @@ def update_current_class_selection( edit_modal_opened, ): """ - This callback is responsible for updating the current class selection when a class is clicked on, or when a keybind is pressed. + This callback is responsible for updating the current class selection when a class is clicked on, + or when a keybind is pressed. """ current_selection = None label_name = None @@ -757,7 +758,9 @@ def populate_load_annotations_dropdown_menu_options(modal_opened, image_src): if not modal_opened: raise PreventUpdate - data = tiled_dataset.DEV_load_exported_json_data(EXPORT_FILE_PATH, USER_NAME, image_src) + data = tiled_dataset.DEV_load_exported_json_data( + EXPORT_FILE_PATH, USER_NAME, image_src + ) if not data: return "No annotations found for the selected data source." @@ -801,8 +804,12 @@ def load_and_apply_selected_annotations(selected_annotation, image_src, img_idx) )["index"] # TODO : when quering from the server, load (data) for user, source, time - data = tiled_dataset.DEV_load_exported_json_data(EXPORT_FILE_PATH, USER_NAME, image_src) - data = tiled_dataset.DEV_filter_json_data_by_timestamp(data, str(selected_annotation_timestamp)) + data = tiled_dataset.DEV_load_exported_json_data( + EXPORT_FILE_PATH, USER_NAME, image_src + ) + data = tiled_dataset.DEV_filter_json_data_by_timestamp( + data, str(selected_annotation_timestamp) + ) data = data[0]["data"] annotations = [] @@ -847,8 +854,10 @@ def populate_classification_results( ): if refresh_tiled: tiled_dataset.refresh_data() - - data_options = [ item for item in tiled_dataset.get_data_project_names() if "seg" not in item] + + data_options = [ + item for item in tiled_dataset.get_data_project_names() if "seg" not in item + ] results = [] value = None checked = False @@ -875,7 +884,15 @@ def populate_classification_results( disabled_toggle = False disabled_slider = False - return results, value, disabled_dropdown, checked, disabled_toggle, disabled_slider, data_options + return ( + results, + value, + disabled_dropdown, + checked, + disabled_toggle, + disabled_slider, + data_options, + ) @callback( diff --git a/callbacks/image_viewer.py b/callbacks/image_viewer.py index 72fbdc51..a8646401 100644 --- a/callbacks/image_viewer.py +++ b/callbacks/image_viewer.py @@ -1,7 +1,4 @@ -import random - import dash -import dash_mantine_components as dmc import numpy as np import plotly.express as px import plotly.graph_objects as go @@ -17,8 +14,6 @@ ctx, ) from dash.exceptions import PreventUpdate -from dash_iconify import DashIconify -from plotly.subplots import make_subplots from constants import ANNOT_ICONS, ANNOT_NOTIFICATION_MSGS, KEYBINDS from utils.data_utils import tiled_dataset @@ -123,7 +118,9 @@ def render_image( ): return [dash.no_update] * 7 + ["hidden"] if str(image_idx + 1) in tiled_dataset.get_annotated_segmented_results(): - result = tiled_dataset.get_data_sequence_by_name(seg_result_selection)[image_idx] + result = tiled_dataset.get_data_sequence_by_name(seg_result_selection)[ + image_idx + ] else: result = None else: @@ -298,7 +295,8 @@ def update_viewfinder(relayout_data, annotation_store): contained within the figure layout, so that if the user zooms out/pans away, they will still be able to see the viewfinder box. """ - # Callback is triggered when the image is first loaded, but the annotation_store is not yet populated so we need to prevent the update + # Callback is triggered when the image is first loaded, but the annotation_store is not yet populated + # so we need to prevent the update if not annotation_store["active_img_shape"]: raise PreventUpdate patched_fig = Patch() @@ -486,7 +484,9 @@ def update_slider_values(project_name, annotation_store): "update_selection_and_image" callback which will update image and slider selection component. """ # Retrieve data shape if project_name is valid and points to a 3d array - data_shape = tiled_dataset.get_data_shape_by_name(project_name) if project_name else None + data_shape = ( + tiled_dataset.get_data_shape_by_name(project_name) if project_name else None + ) disable_slider = data_shape is None if not disable_slider: # TODO: Assuming that all slices have the same image shape diff --git a/callbacks/segmentation.py b/callbacks/segmentation.py index ce425a95..69a206c1 100644 --- a/callbacks/segmentation.py +++ b/callbacks/segmentation.py @@ -3,13 +3,11 @@ import uuid import dash_mantine_components as dmc -import numpy as np import requests from dash import ALL, Input, Output, State, callback, no_update from dash.exceptions import PreventUpdate from utils.data_utils import tiled_dataset -from utils.annotations import Annotations MODE = os.getenv("MODE", "") diff --git a/components/annotation_class.py b/components/annotation_class.py index cefbb6f3..a8556099 100644 --- a/components/annotation_class.py +++ b/components/annotation_class.py @@ -176,7 +176,8 @@ def annotation_class_item(class_color, class_label, existing_ids, data=None): children=[ dmc.Center( dmc.Text( - "This action will permanently clear all annotations from this class. Are you sure you want to proceed?", + "This action will permanently clear all annotations from this class." + + " Are you sure you want to proceed?", ) ), dmc.Space(h=10), diff --git a/components/control_bar.py b/components/control_bar.py index dfca3906..b4ab2b0e 100644 --- a/components/control_bar.py +++ b/components/control_bar.py @@ -76,7 +76,7 @@ def layout(): "majesticons:data-line", "data-select", id="data-selection-controls", - children=[ + children=[ dmc.Space(h=5), _control_item( "Dataset", @@ -86,7 +86,11 @@ def layout(): dmc.Select( id="project-name-src", data=DATA_OPTIONS, - value=DATA_OPTIONS[0] if DATA_OPTIONS else None, + value=( + DATA_OPTIONS[0] + if DATA_OPTIONS + else None + ), placeholder="Select an image to view...", ), dmc.ActionIcon( @@ -401,7 +405,8 @@ def layout(): id="delete-all-warning", children=[ dmc.Text( - "This action will permanently clear all annotations on this image frame. Are you sure you want to proceed?" + "This action will permanently clear all annotations on this image frame." + + " Are you sure you want to proceed?" ), dmc.Space(h=20), dmc.Group( diff --git a/components/image_viewer.py b/components/image_viewer.py index 8b82c780..36a88f24 100644 --- a/components/image_viewer.py +++ b/components/image_viewer.py @@ -1,4 +1,3 @@ -import dash_mantine_components as dmc from dash import dcc, html from utils.plot_utils import blank_fig diff --git a/utils/annotations.py b/utils/annotations.py index 5fd7b5c6..765ac73a 100644 --- a/utils/annotations.py +++ b/utils/annotations.py @@ -1,5 +1,4 @@ import io -import math import zipfile import numpy as np diff --git a/utils/data_utils.py b/utils/data_utils.py index b9a41bca..bb54d295 100644 --- a/utils/data_utils.py +++ b/utils/data_utils.py @@ -10,7 +10,6 @@ from utils.annotations import Annotations - load_dotenv() DATA_TILED_URI = os.getenv("DATA_TILED_URI") @@ -18,15 +17,23 @@ class TiledDataLoader: - def __init__(self, data_tiled_uri=DATA_TILED_URI, data_tiled_api_key=DATA_TILED_API_KEY): + def __init__( + self, data_tiled_uri=DATA_TILED_URI, data_tiled_api_key=DATA_TILED_API_KEY + ): self.data_tiled_uri = data_tiled_uri self.data_tiled_api_key = data_tiled_api_key - self.data = from_uri(self.data_tiled_uri, api_key=self.data_tiled_api_key, timeout=httpx.Timeout(30.0)) - - - def refresh_data(self): - self.data = from_uri(self.data_tiled_uri, api_key=self.data_tiled_api_key, timeout=httpx.Timeout(30.0)) + self.data = from_uri( + self.data_tiled_uri, + api_key=self.data_tiled_api_key, + timeout=httpx.Timeout(30.0), + ) + def refresh_data(self): + self.data = from_uri( + self.data_tiled_uri, + api_key=self.data_tiled_api_key, + timeout=httpx.Timeout(30.0), + ) def get_data_project_names(self): """ @@ -40,7 +47,6 @@ def get_data_project_names(self): ] return project_names - def get_data_sequence_by_name(self, project_name): """ Data sequences may be given directly inside the main client container, @@ -69,7 +75,6 @@ def get_data_sequence_by_name(self, project_name): return sequence_client return None - def get_data_shape_by_name(self, project_name): """ Retrieve shape of the data @@ -79,7 +84,6 @@ def get_data_shape_by_name(self, project_name): return project_container.shape return None - @staticmethod def get_annotated_segmented_results(json_file_path="exported_annotation_data.json"): annotated_slices = [] @@ -91,7 +95,6 @@ def get_annotated_segmented_results(json_file_path="exported_annotation_data.jso annotated_slices = list(json_data["data"][0]["annotations"].keys()) return annotated_slices - @staticmethod def DEV_load_exported_json_data(file_path, USER_NAME, PROJECT_NAME): """ @@ -121,12 +124,10 @@ def DEV_load_exported_json_data(file_path, USER_NAME, PROJECT_NAME): return data - @staticmethod def DEV_filter_json_data_by_timestamp(data, timestamp): return [data for data in data if data["time"] == timestamp] - def save_annotations_data(self, global_store, all_annotations, project_name): """ Transforms annotations data to a pixelated mask and outputs to @@ -158,4 +159,3 @@ def save_annotations_data(self, global_store, all_annotations, project_name): tiled_dataset = TiledDataLoader() - diff --git a/utils/download_sample_data.py b/utils/download_sample_data.py index 13ae52eb..4babdf01 100644 --- a/utils/download_sample_data.py +++ b/utils/download_sample_data.py @@ -1,6 +1,7 @@ -import requests import os +import requests + def DEV_download_google_sample_data(): """ diff --git a/utils/plot_utils.py b/utils/plot_utils.py index e2b72445..55a7dd18 100644 --- a/utils/plot_utils.py +++ b/utils/plot_utils.py @@ -6,8 +6,6 @@ from dash_iconify import DashIconify from skimage.transform import resize -from constants import ANNOT_ICONS - def blank_fig(): """ @@ -32,7 +30,8 @@ def downscale_view( """ This function takes pan+zoom location in the original image and downscales it relatively to viewfinder's lower resolution. params: - x0_original, y0_original, x1_original, y1_original: coordinates of the pan+zoom box in the original image - obtained from relayoutData + x0_original, y0_original, x1_original, y1_original: coordinates of the pan+zoom box in the original image + - obtained from relayoutData active_image_size: size of the original image (height, width) in pixels downscaled_image_size: size of the viewfinder (height, width) in pixels returns: From 09683d6bca2523c52ca8dc90d09dce26ce064170 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Wiebke=20K=C3=B6pp?= Date: Tue, 20 Feb 2024 17:10:46 -0800 Subject: [PATCH 4/8] Delete `data.tmp` --- data/.tmp | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 data/.tmp diff --git a/data/.tmp b/data/.tmp deleted file mode 100644 index e69de29b..00000000 From 32adcf2f5dfef9ba659fcd0b763ce931e024eb79 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Wiebke=20K=C3=B6pp?= Date: Tue, 20 Feb 2024 18:51:46 -0800 Subject: [PATCH 5/8] :bug: Adapt local annotations file path to `exported_annotation_data.json` This omits the just deleted /data directory. This file and corresponding variables no longer be used at all once #160 is addressed. --- callbacks/control_bar.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/callbacks/control_bar.py b/callbacks/control_bar.py index 700a7dea..9d7d438d 100644 --- a/callbacks/control_bar.py +++ b/callbacks/control_bar.py @@ -30,7 +30,7 @@ from utils.plot_utils import generate_notification, generate_notification_bg_icon_col # TODO - temporary local file path and user for annotation saving and exporting -EXPORT_FILE_PATH = os.getenv("EXPORT_FILE_PATH", "data/exported_annotation_data.json") +EXPORT_FILE_PATH = os.getenv("EXPORT_FILE_PATH", "exported_annotation_data.json") USER_NAME = os.getenv("USER_NAME", "user1") # Create an empty file if it doesn't exist From 246cfa34f9d6445b317ff242cadd0e7d191b23fa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Wiebke=20K=C3=B6pp?= Date: Thu, 22 Feb 2024 08:26:00 -0800 Subject: [PATCH 6/8] Add additional pre-commit hooks for trimming trailing white spaces, fixing ends of files, and checking for broken symlinks, case and merge conflicts, valid python and yaml --- .pre-commit-config.yaml | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index cad41cce..cc2ea1e5 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,17 @@ default_language_version: python: python3 repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.5.0 + hooks: + - id: trailing-whitespace + - id: end-of-file-fixer + - id: check-ast + - id: check-case-conflict + - id: check-merge-conflict + - id: check-symlinks + - id: check-yaml + - id: debug-statements # Using this mirror lets us use mypyc-compiled black, which is about 2x faster - repo: https://github.com/psf/black-pre-commit-mirror rev: 24.2.0 From 8106e782c8e9833fae4205b10c984bea503ed5f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Wiebke=20K=C3=B6pp?= Date: Thu, 22 Feb 2024 08:27:02 -0800 Subject: [PATCH 7/8] Result of `pre-commit run --all-files` with additional pre-commit hooks --- .env.example | 18 +++++++++--------- .flake8 | 4 ++-- .github/workflows/publish-image.yml | 2 +- .github/workflows/test-lint.yml | 2 +- .gitignore | 2 +- COPYRIGHT.txt | 2 +- README.md | 8 ++++---- assets/functions.js | 2 +- assets/style.css | 2 +- exported_annotation_data.json | 2 +- pyproject.toml | 2 +- requirements.txt | 2 +- tiled_serve_dir.sh | 2 +- 13 files changed, 25 insertions(+), 25 deletions(-) diff --git a/.env.example b/.env.example index de0656b9..dd72de46 100644 --- a/.env.example +++ b/.env.example @@ -1,11 +1,11 @@ # The URI of a container in a Tiled server with data to be segmented -# Replace with the URI for such a container. +# Replace with the URI for such a container. # Examples are: -# the 'reconstruction' container of the public server, containing tomography reconstructions: +# the 'reconstruction' container of the public server, containing tomography reconstructions: # 'https://tiled-seg.als.lbl.gov/api/v1/metadata/reconstruction' -# the root container of a local server: +# the root container of a local server: # 'http://localhost:8000/' -# the 'processed' container of a server running in a docker container: +# the 'processed' container of a server running in a docker container: # 'http://tiled:8000/api/v1/metadata/processed' DATA_TILED_URI= # API key for accessing the Tiled server and container from DATA_TILED_URI @@ -13,18 +13,18 @@ DATA_TILED_URI= DATA_TILED_API_KEY= # The URI of a container in a Tiled server where we can store mask information -# Replace with the URL of your Tiled server. +# Replace with the URL of your Tiled server. # You will need write-access to this container. MASK_TILED_URI= # API key for accessing the Tiled server and container from MASK_TILED_URI -# Replace with your API key +# Replace with your API key MASK_TILED_API_KEY= # The URI of a Tiled server where segmentation results can be retrieved # The Tiled server will most likely be the same as the one used for storing masks -# This top-level URI is not used directly. +# This top-level URI is not used directly. # Instead we expect ML jobs to return one or more URIs pointing to specific results -# Replace with the URL of your Tiled server. +# Replace with the URL of your Tiled server. SEG_TILED_URI= # API key for accessing the Tiled server from SEG_TILED_URI # Replace with your API key @@ -37,4 +37,4 @@ MODE='dev' # Basic authentication for segmentation application when deploying on a publicly accessible server USER_NAME= -USER_PASSWORD= \ No newline at end of file +USER_PASSWORD= diff --git a/.flake8 b/.flake8 index 77dac34a..a9f89c57 100644 --- a/.flake8 +++ b/.flake8 @@ -1,7 +1,7 @@ [flake8] -# 127 is width of the Github code viewer, +# 127 is width of the Github code viewer, # black default is 88 so this will only warn about comments >127 max-line-length = 127 # Ignore errors due to incompatibility with black #https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html -extend-ignore = E203,E701 \ No newline at end of file +extend-ignore = E203,E701 diff --git a/.github/workflows/publish-image.yml b/.github/workflows/publish-image.yml index 50673e66..acd751fa 100644 --- a/.github/workflows/publish-image.yml +++ b/.github/workflows/publish-image.yml @@ -42,4 +42,4 @@ jobs: file: Dockerfile push: true tags: ${{ steps.meta.outputs.tags }} - labels: ${{ steps.meta.outputs.labels }} \ No newline at end of file + labels: ${{ steps.meta.outputs.labels }} diff --git a/.github/workflows/test-lint.yml b/.github/workflows/test-lint.yml index 50bcda28..e041300a 100644 --- a/.github/workflows/test-lint.yml +++ b/.github/workflows/test-lint.yml @@ -31,4 +31,4 @@ jobs: black . --check - name: Run pytest run: | - python -m pytest \ No newline at end of file + python -m pytest diff --git a/.gitignore b/.gitignore index 5a4b6368..478f984b 100644 --- a/.gitignore +++ b/.gitignore @@ -23,4 +23,4 @@ env *.tiff *.tif -.env \ No newline at end of file +.env diff --git a/COPYRIGHT.txt b/COPYRIGHT.txt index ff3b3b03..b4cb5878 100644 --- a/COPYRIGHT.txt +++ b/COPYRIGHT.txt @@ -10,5 +10,5 @@ NOTICE. This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the -Software to reproduce, distribute copies to the public, prepare derivative +Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit others to do so. diff --git a/README.md b/README.md index 24aec47c..7b937054 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,9 @@ # Dash App for Segmentation of High-Resolution Images [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1)](https://pycqa.github.io/isort/) -This application is built using Plotly's [Dash](https://dash.plotly.com/) framework and provides a web-based interface for visualizing and annotating high resolution images output from [ALS](https://als.lbl.gov/) beamlines. +This application is built using Plotly's [Dash](https://dash.plotly.com/) framework and provides a web-based interface for visualizing and annotating high resolution images output from [ALS](https://als.lbl.gov/) beamlines. -Image data is accessed via a [Tiled](https://github.com/bluesky/tiled) client, which provides chunkwise access to multidimensional TIFF sequences. +Image data is accessed via a [Tiled](https://github.com/bluesky/tiled) client, which provides chunkwise access to multidimensional TIFF sequences. ![plot](assets/preview.png) @@ -17,7 +17,7 @@ Image data is accessed via a [Tiled](https://github.com/bluesky/tiled) client, w pip install -r requirements.txt ``` -and +and ``` pip install -r requirements-dev.txt @@ -32,7 +32,7 @@ DASH_DEPLOYMENT_LOC='Local' MODE='dev' ``` -3. Start a local server: +3. Start a local server: ``` python app.py diff --git a/assets/functions.js b/assets/functions.js index 5edbf812..101845dc 100644 --- a/assets/functions.js +++ b/assets/functions.js @@ -49,4 +49,4 @@ function remove_focus() { sliderContainer.addEventListener('blur', () => { sliderContainer.blur(); }); -} \ No newline at end of file +} diff --git a/assets/style.css b/assets/style.css index 046caacc..da432a26 100644 --- a/assets/style.css +++ b/assets/style.css @@ -142,4 +142,4 @@ body { /* used to hide viewfinder */ .hidden { display: none; -} \ No newline at end of file +} diff --git a/exported_annotation_data.json b/exported_annotation_data.json index ae714bb3..644c849a 100644 --- a/exported_annotation_data.json +++ b/exported_annotation_data.json @@ -1 +1 @@ -{"user": "user1", "source": "rec20190524_085542_clay_testZMQ_8bit", "time": "2023-11-03-01:13:15", "data": "[{\"annotations\": {\"10\": [{\"editable\": true, \"visible\": true, \"showlegend\": false, \"legend\": \"legend\", 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=?UTF-8?q?Wiebke=20K=C3=B6pp?= Date: Thu, 22 Feb 2024 08:29:13 -0800 Subject: [PATCH 8/8] Remove `tiled[all]` from `requirements-dev.txt, pin version in `README.md` --- README.md | 2 +- requirements-dev.txt | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index 7b937054..37dc3ecd 100644 --- a/README.md +++ b/README.md @@ -43,7 +43,7 @@ python app.py For local testing of just the annotation functionality, developers may also choose to set up a local Tiled server with access to minimal datasets (eg. in the case that the remote server is down). To download some sample data and serve it with a local Tiled serve -1. Additionally install the Tiled server components with `pip install "tiled[server]"`. +1. Additionally install the Tiled server components with `pip install "tiled[server]==0.1.0a114"`. 2. Set the input Tiled URI to localhost, e.g. set `DATA_TILED_URI`, to `http://localhost:8000/` within the `.env` file (or within your environmental variables), and use the result of a key generator (e.g. with `python3 -c "import secrets; print(secrets.token_hex(32))"`) for the key entry `DATA_TILED_API_KEY` 2. Run the script `python3 utils/download_sample_data.py`. This will create a `data/` directory and download 2 sample projects with 2 images each. 3. Run `/tiled_serve_dir.sh`. diff --git a/requirements-dev.txt b/requirements-dev.txt index e0e86de3..37c55bc8 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -1,6 +1,5 @@ black==24.2.0 flake8==7.0.0 -tiled[all]==0.1.0a114 pytest pytest-mock isort==5.13.2