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Merge pull request #192 from kushalbakshi/dev_widget
Add ROI drawing widget
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@@ -124,3 +124,6 @@ example_data | |
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| # vscode | ||
| *.code-workspace | ||
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| # dash widget | ||
| file_system_backend | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,228 @@ | ||
| import yaml | ||
| import datajoint as dj | ||
| import numpy as np | ||
| import plotly.express as px | ||
| import plotly.graph_objects as go | ||
| from dash import no_update | ||
| from dash_extensions.enrich import ( | ||
| DashProxy, | ||
| Input, | ||
| Output, | ||
| State, | ||
| html, | ||
| dcc, | ||
| Serverside, | ||
| ServersideOutputTransform, | ||
| ) | ||
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| from .utilities import * | ||
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| logger = dj.logger | ||
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| def draw_rois(db_prefix: str): | ||
| scan = dj.create_virtual_module("scan", f"{db_prefix}scan") | ||
| imaging = dj.create_virtual_module("imaging", f"{db_prefix}imaging") | ||
| all_keys = (imaging.MotionCorrection).fetch("KEY") | ||
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| colors = {"background": "#111111", "text": "#00a0df"} | ||
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| app = DashProxy(transforms=[ServersideOutputTransform()]) | ||
| app.layout = html.Div( | ||
| [ | ||
| html.H2("Draw ROIs", style={"color": colors["text"]}), | ||
| html.Label( | ||
| "Select data key from dropdown", style={"color": colors["text"]} | ||
| ), | ||
| dcc.Dropdown( | ||
| id="toplevel-dropdown", options=[str(key) for key in all_keys] | ||
| ), | ||
| html.Br(), | ||
| html.Div( | ||
| [ | ||
| html.Button( | ||
| "Load Image", | ||
| id="load-image-button", | ||
| style={"margin-right": "20px"}, | ||
| ), | ||
| dcc.RadioItems( | ||
| id="image-type-radio", | ||
| options=[ | ||
| {"label": "Average Image", "value": "average_image"}, | ||
| { | ||
| "label": "Max Projection Image", | ||
| "value": "max_projection_image", | ||
| }, | ||
| ], | ||
| value="average_image", | ||
| labelStyle={"display": "inline-block", "margin-right": "10px"}, | ||
| style={"display": "inline-block", "color": colors["text"]}, | ||
| ), | ||
| html.Div( | ||
| [ | ||
| html.Button("Submit Curated Masks", id="submit-button"), | ||
| ], | ||
| style={ | ||
| "textAlign": "right", | ||
| "flex": "1", | ||
| "display": "inline-block", | ||
| }, | ||
| ), | ||
| ], | ||
| style={ | ||
| "display": "flex", | ||
| "justify-content": "flex-start", | ||
| "align-items": "center", | ||
| }, | ||
| ), | ||
| html.Br(), | ||
| html.Br(), | ||
| html.Div( | ||
| [ | ||
| dcc.Graph( | ||
| id="avg-image", | ||
| config={ | ||
| "modeBarButtonsToAdd": [ | ||
| "drawclosedpath", | ||
| "drawrect", | ||
| "drawcircle", | ||
| "drawline", | ||
| "eraseshape", | ||
| ], | ||
| }, | ||
| style={"width": "100%", "height": "100%"}, | ||
| ) | ||
| ], | ||
| style={ | ||
| "display": "flex", | ||
| "justify-content": "center", | ||
| "align-items": "center", | ||
| "padding": "0.0", | ||
| "margin": "auto", | ||
| }, | ||
| ), | ||
| html.Pre(id="annotations"), | ||
| html.Div(id="button-output"), | ||
| dcc.Store(id="store-key"), | ||
| dcc.Store(id="store-mask"), | ||
| dcc.Store(id="store-movie"), | ||
| html.Div(id="submit-output"), | ||
| ] | ||
| ) | ||
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| @app.callback( | ||
| Output("store-key", "value"), | ||
| Input("toplevel-dropdown", "value"), | ||
| ) | ||
| def store_key(value): | ||
| if value is not None: | ||
| return Serverside(value) | ||
| else: | ||
| return no_update | ||
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| @app.callback( | ||
| Output("avg-image", "figure"), | ||
| Output("store-movie", "average_images"), | ||
| State("store-key", "value"), | ||
| Input("load-image-button", "n_clicks"), | ||
| Input("image-type-radio", "value"), | ||
| prevent_initial_call=True, | ||
| ) | ||
| def create_figure(value, render_n_clicks, image_type): | ||
| if render_n_clicks is not None: | ||
| if image_type == "average_image": | ||
| summary_images = ( | ||
| imaging.MotionCorrection.Summary & yaml.safe_load(value) | ||
| ).fetch("average_image") | ||
| else: | ||
| summary_images = ( | ||
| imaging.MotionCorrection.Summary & yaml.safe_load(value) | ||
| ).fetch("max_proj_image") | ||
| average_images = [image.astype("float") for image in summary_images] | ||
| roi_contours = get_contours(yaml.safe_load(value), db_prefix) | ||
| logger.info("Generating figure.") | ||
| fig = px.imshow( | ||
| np.asarray(average_images), | ||
| animation_frame=0, | ||
| binary_string=True, | ||
| labels=dict(animation_frame="plane"), | ||
| ) | ||
| for contour in roi_contours: | ||
| # Note: contour[:, 1] are x-coordinates, contour[:, 0] are y-coordinates | ||
| fig.add_trace( | ||
| go.Scatter( | ||
| x=contour[:, 1], # Plotly uses x, y order for coordinates | ||
| y=contour[:, 0], | ||
| mode="lines", # Display as lines (not markers) | ||
| line=dict(color="white", width=0.5), # Set line color and width | ||
| showlegend=False, # Do not show legend for each contour | ||
| ) | ||
| ) | ||
| fig.update_layout( | ||
| dragmode="drawrect", | ||
| autosize=True, | ||
| height=550, | ||
| newshape=dict(opacity=0.6, fillcolor="#00a0df"), | ||
| plot_bgcolor=colors["background"], | ||
| paper_bgcolor=colors["background"], | ||
| font_color=colors["text"], | ||
| ) | ||
| fig.update_annotations(bgcolor="#00a0df") | ||
| else: | ||
| return no_update | ||
| return fig, Serverside(average_images) | ||
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| @app.callback( | ||
| Output("store-mask", "annotation_list"), | ||
| Input("avg-image", "relayoutData"), | ||
| prevent_initial_call=True, | ||
| ) | ||
| def on_relayout(relayout_data): | ||
| if not relayout_data: | ||
| return no_update | ||
| else: | ||
| if "shapes" in relayout_data: | ||
| global shape_type | ||
| try: | ||
| shape_type = relayout_data["shapes"][-1]["type"] | ||
| return Serverside(relayout_data) | ||
| except IndexError: | ||
| return no_update | ||
| elif any(["shapes" in key for key in relayout_data]): | ||
| return Serverside(relayout_data) | ||
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| @app.callback( | ||
| Output("submit-output", "children"), | ||
| Input("submit-button", "n_clicks"), | ||
| State("store-mask", "annotation_list"), | ||
| State("store-key", "value"), | ||
| ) | ||
| def submit_annotations(n_clicks, annotation_list, value): | ||
| x_mask_li = [] | ||
| y_mask_li = [] | ||
| if n_clicks is not None: | ||
| if annotation_list: | ||
| if "shapes" in annotation_list: | ||
| logger.info("Creating Masks.") | ||
| shapes = [d["type"] for d in annotation_list["shapes"]] | ||
| for shape, annotation in zip(shapes, annotation_list["shapes"]): | ||
| mask = create_mask(annotation, shape) | ||
| y_mask_li.append(mask[0]) | ||
| x_mask_li.append(mask[1]) | ||
| print("Masks created") | ||
| insert_into_database( | ||
| scan, imaging, yaml.safe_load(value), x_mask_li, y_mask_li | ||
| ) | ||
| else: | ||
| logger.warn( | ||
| "Incorrect annotation list format. This is a known bug. Please draw a line anywhere on the image and click `Submit Curated Masks`. It will be ignored in the final submission but will format the list correctly." | ||
| ) | ||
| return no_update | ||
| else: | ||
| logger.warn("No annotations to submit.") | ||
| return no_update | ||
| else: | ||
| return no_update | ||
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| return app |
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