Spaces:
Running
Running
Ashwin V. Mohanan
commited on
Commit
·
5015c53
1
Parent(s):
ed479a9
Variable probability threshold
Browse files- app/tabs/submit.py +94 -31
- app/tabs/visualizer.py +5 -4
app/tabs/submit.py
CHANGED
@@ -9,6 +9,7 @@ from PIL import Image
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from dawsonia import io
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from dawsonia import digitize
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from dawsonia.ml import ml
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import gradio as gr
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from gradio_modal import Modal
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import numpy as np
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@@ -40,16 +41,22 @@ PIPELINES: dict[str, dict[str, str]] = {
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"härnösand": dict(
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url="https://git.smhi.se/ai-for-obs/data/-/raw/688c04f13e8e946962792fe4b4e0ded98800b154/raw_zarr/H%C3%84RN%C3%96SAND/DAGBOK_H%C3%A4rn%C3%B6sand_Station_1934.zarr.zip",
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known_hash="sha256:a58fdb6521214d0bd569c9325ce78d696738de28ce6ec869cde0d46616b697f2",
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-
)
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}
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def run_dawsonia(
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table_fmt_config_override,
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):
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if book is None:
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raise ValueError("You need to select / upload the pages to digitize")
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-
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progress(0, desc="Dawsonia: starting")
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model_path = Path("data/models/dawsonia/2024-07-02")
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@@ -79,7 +86,11 @@ def run_dawsonia(
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output_path_page = output_path_book / str(page_number)
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gr.Info(f"Digitizing {page_number = }")
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if
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digitize.digitize_page_and_write_output(
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book,
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init_data,
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@@ -87,48 +98,66 @@ def run_dawsonia(
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date_str=f"0000-page-{page_number}",
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model_path=model_path,
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model_predict=ml.model_predict,
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-
prob_thresh=
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output_path_page=output_path_page,
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output_text_fmt=False,
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debug=False,
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)
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progress_value = (page_number - first_page) / max(1, last_page - first_page)
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if results := read_page(
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page, im = results
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collection.append(page)
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images.append(im)
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else:
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gr.Info(f"No tables detected in {page_number = }")
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-
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gr.Info("Pages were succesfully digitized ✨")
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# yield collection, images
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yield collection, gr.skip()
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def read_page(
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-
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print(stats)
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progress(progress_value, desc=f"Dawsonia: {stats!s:.50}")
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if stats.tables_detected > 0:
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values_df = pd.read_parquet((output_path_book / prefix).with_suffix(".parquet"))
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table_meta = json.loads(
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(output_path_book / "table_meta" / prefix).with_suffix(".json").read_text()
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)
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with Image.open(
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image_path:=(output_path_book / "pages" / prefix).with_suffix(".webp")
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) as im:
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width = im.width
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height = im.height
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values_array = values_df.values.flatten()
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-
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-
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)
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cells = [
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make_cell(value, bbox)
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]
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return Page(width, height, cells, im_path_from_gallery or str(image_path)), im
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@@ -136,10 +165,10 @@ def read_page(output_path_book: Path, prefix: str, progress, progress_value, im_
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def make_cell(value: str, bbox: NDArray[np.int64]):
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y, x, h, w = bbox
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xmin, ymin = x-w//2, y-h//2
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xmax, ymax = x+w//2, y+h//2
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polygon = (xmin,ymin), (xmax, ymin), (xmax, ymax), (xmin, ymax), (xmin,ymin)
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return TableCell(polygon, text_x=x, text_y=y, text=value)
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def all_example_images() -> list[str]:
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@@ -171,7 +200,12 @@ def get_selected_example_image(
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first, last, book = io.read_book(book_path)
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book._name = name
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book.size_cell = [1.0, 1.0, 1.0, 1.0]
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-
return
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def overwrite_table_format_file(book: io.Book, book_path, table_fmt: str):
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@@ -184,9 +218,8 @@ def overwrite_table_format_file(book: io.Book, book_path, table_fmt: str):
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with gr.Blocks() as submit:
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gr.Markdown("# Upload")
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gr.Markdown(
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"Select or upload the image you want to transcribe. You can upload up to five images at a time."
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)
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batch_book_state = gr.State()
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@@ -197,11 +230,11 @@ with gr.Blocks() as submit:
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with gr.Row(equal_height=True):
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with gr.Column(scale=5):
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batch_image_gallery = gr.Gallery(
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file_types=["
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label="
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interactive=True,
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object_fit="scale-down",
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scale=1,
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)
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with gr.Column(scale=2):
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@@ -215,6 +248,7 @@ with gr.Blocks() as submit:
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object_fit="scale-down",
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min_width=250,
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)
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with Modal(visible=False) as edit_table_fmt_modal:
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with gr.Column():
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@@ -223,7 +257,9 @@ with gr.Blocks() as submit:
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"Write a custom table format, overriding the default one. "
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"Click on the **Save** button when you are done."
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)
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save_tf_button = gr.Button(
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gr.HTML(
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(
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"<a href='https://dawsonia.readthedocs.io/en/latest/user_guide/misc.html#table-formats' target='_blank'>"
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@@ -235,6 +271,15 @@ with gr.Blocks() as submit:
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)
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table_fmt_config_override = gr.Code("", language="python")
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with gr.Row():
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run_button = gr.Button("Digitize", variant="primary", scale=0, min_width=200)
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edit_table_fmt_button = gr.Button(
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@@ -246,7 +291,12 @@ with gr.Blocks() as submit:
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examples.select(
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get_selected_example_image,
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(first_page, last_page),
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(
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trigger_mode="always_last",
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)
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@@ -255,21 +305,34 @@ with gr.Blocks() as submit:
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outputs=[batch_image_gallery],
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)
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def validate_images(images):
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if len(images) > MAX_IMAGES:
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gr.Warning(f"Maximum images you can upload is set to: {MAX_IMAGES}")
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return gr.update(value=None)
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-
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gr.Warning(
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raise NotImplementedError("WIP")
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return images
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-
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run_button.click(
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fn=run_dawsonia,
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inputs=(
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outputs=(collection_submit_state, batch_image_gallery),
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)
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## Table formats modal dialog box
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edit_table_fmt_button.click(lambda: Modal(visible=True), None, edit_table_fmt_modal)
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save_tf_button.click(
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overwrite_table_format_file,
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from dawsonia import io
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from dawsonia import digitize
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from dawsonia.ml import ml
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+
from dawsonia.typing import Probability
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import gradio as gr
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from gradio_modal import Modal
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import numpy as np
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"härnösand": dict(
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url="https://git.smhi.se/ai-for-obs/data/-/raw/688c04f13e8e946962792fe4b4e0ded98800b154/raw_zarr/H%C3%84RN%C3%96SAND/DAGBOK_H%C3%A4rn%C3%B6sand_Station_1934.zarr.zip",
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known_hash="sha256:a58fdb6521214d0bd569c9325ce78d696738de28ce6ec869cde0d46616b697f2",
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+
),
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}
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def run_dawsonia(
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+
table_fmt_config_override,
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+
first_page,
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+
last_page,
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+
prob_thresh,
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+
book,
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gallery,
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progress=gr.Progress(),
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):
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if book is None:
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raise ValueError("You need to select / upload the pages to digitize")
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+
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progress(0, desc="Dawsonia: starting")
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model_path = Path("data/models/dawsonia/2024-07-02")
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output_path_page = output_path_book / str(page_number)
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gr.Info(f"Digitizing {page_number = }")
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if (
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not (output_path_book / str(page_number))
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.with_suffix(".parquet")
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.exists()
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):
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digitize.digitize_page_and_write_output(
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book,
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init_data,
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date_str=f"0000-page-{page_number}",
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model_path=model_path,
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model_predict=ml.model_predict,
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+
prob_thresh=prob_thresh,
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output_path_page=output_path_page,
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output_text_fmt=False,
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debug=False,
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)
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progress_value = (page_number - first_page) / max(1, last_page - first_page)
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if results := read_page(
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output_path_book,
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str(page_number),
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prob_thresh,
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progress,
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progress_value,
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): # , im_from_gallery[0])
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page, im = results
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collection.append(page)
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images.append(im)
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else:
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gr.Info(f"No tables detected in {page_number = }")
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gr.Info("Pages were succesfully digitized ✨")
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# yield collection, images
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yield collection, gr.skip()
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def read_page(
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output_path_book: Path,
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prefix: str,
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prob_thresh: float,
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progress,
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progress_value,
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im_path_from_gallery: str = "",
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):
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stats = digitize.Statistics.from_json(
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(output_path_book / "statistics" / prefix).with_suffix(".json")
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)
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print(stats)
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progress(progress_value, desc=f"Dawsonia: {stats!s:.50}")
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if stats.tables_detected > 0:
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values_df = pd.read_parquet((output_path_book / prefix).with_suffix(".parquet"))
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+
prob_df = pd.read_parquet(
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(output_path_book / "probablities" / prefix).with_suffix(".parquet")
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)
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table_meta = json.loads(
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(output_path_book / "table_meta" / prefix).with_suffix(".json").read_text()
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)
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with Image.open(
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image_path := (output_path_book / "pages" / prefix).with_suffix(".webp")
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) as im:
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width = im.width
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height = im.height
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values_array = values_df.values.flatten()
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prob_array = prob_df.values.flatten()
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bbox_array = np.hstack(table_meta["table_positions"]).reshape(-1, 4)
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cells = [
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make_cell(value, bbox)
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for value, prob, bbox in zip(values_array, prob_array, bbox_array)
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if prob > prob_thresh
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]
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return Page(width, height, cells, im_path_from_gallery or str(image_path)), im
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def make_cell(value: str, bbox: NDArray[np.int64]):
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y, x, h, w = bbox
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+
xmin, ymin = x - w // 2, y - h // 2
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+
xmax, ymax = x + w // 2, y + h // 2
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polygon = (xmin, ymin), (xmax, ymin), (xmax, ymax), (xmin, ymax), (xmin, ymin)
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return TableCell(polygon, text_x=x - w // 4, text_y=y, text=value)
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def all_example_images() -> list[str]:
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first, last, book = io.read_book(book_path)
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book._name = name
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book.size_cell = [1.0, 1.0, 1.0, 1.0]
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return (
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[book.read_image(pg) for pg in range(first_page, last_page)],
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book,
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book_path,
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station_tf.read_text(),
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)
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def overwrite_table_format_file(book: io.Book, book_path, table_fmt: str):
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with gr.Blocks() as submit:
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gr.Markdown(
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"🛈 Select or upload the image you want to transcribe. You can upload up to five images at a time."
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)
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batch_book_state = gr.State()
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with gr.Row(equal_height=True):
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with gr.Column(scale=5):
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batch_image_gallery = gr.Gallery(
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# file_types=[".pdf", ".zarr.zip"],
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label="Book to digitize (should be a .pdf or .zarr.zip file)",
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interactive=True,
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object_fit="scale-down",
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scale=1.0,
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)
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with gr.Column(scale=2):
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object_fit="scale-down",
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min_width=250,
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)
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upload_button = gr.UploadButton(min_width=200)
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with Modal(visible=False) as edit_table_fmt_modal:
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with gr.Column():
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"Write a custom table format, overriding the default one. "
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"Click on the **Save** button when you are done."
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)
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+
save_tf_button = gr.Button(
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"Save", variant="primary", scale=0, min_width=200
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)
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gr.HTML(
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(
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"<a href='https://dawsonia.readthedocs.io/en/latest/user_guide/misc.html#table-formats' target='_blank'>"
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)
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table_fmt_config_override = gr.Code("", language="python")
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+
with gr.Row():
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prob_thresh = gr.Slider(
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minimum=0.0,
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maximum=1.0,
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value=0.75,
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step=0.05,
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+
label="Prediction probability threshold",
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)
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+
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with gr.Row():
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run_button = gr.Button("Digitize", variant="primary", scale=0, min_width=200)
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edit_table_fmt_button = gr.Button(
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examples.select(
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get_selected_example_image,
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(first_page, last_page),
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+
(
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+
batch_image_gallery,
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+
batch_book_state,
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+
batch_book_path_state,
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+
table_fmt_config_override,
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+
),
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trigger_mode="always_last",
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)
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outputs=[batch_image_gallery],
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)
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def validate_images(images):
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+
print(images)
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if len(images) > MAX_IMAGES:
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gr.Warning(f"Maximum images you can upload is set to: {MAX_IMAGES}")
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return gr.update(value=None)
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+
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+
gr.Warning(
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+
"Digitizing uploaded images is not implemented yet! Work in progress!"
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+
)
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raise NotImplementedError("WIP")
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return images
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+
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run_button.click(
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fn=run_dawsonia,
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+
inputs=(
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+
table_fmt_config_override,
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+
first_page,
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+
last_page,
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+
prob_thresh,
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+
batch_book_state,
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+
batch_image_gallery,
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+
),
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outputs=(collection_submit_state, batch_image_gallery),
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)
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## Table formats modal dialog box
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edit_table_fmt_button.click(lambda: Modal(visible=True), None, edit_table_fmt_modal)
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save_tf_button.click(
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+
overwrite_table_format_file,
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+
(batch_book_state, batch_book_path_state, table_fmt_config_override),
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+
(batch_book_state,),
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+
)
|
app/tabs/visualizer.py
CHANGED
@@ -26,11 +26,13 @@ class Page(NamedTuple):
|
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26 |
|
27 |
Collection: TypeAlias = list[Page]
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28 |
|
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29 |
def render_image(collection: Collection, current_page_index: int) -> str:
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return _IMAGE_TEMPLATE.render(
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page=collection[current_page_index],
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)
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def toggle_navigation_button(collection: Collection):
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visible = len(collection) > 1
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return gr.update(visible=visible)
|
@@ -62,9 +64,8 @@ def update_image_caption(collection: Collection, current_page_index):
|
|
62 |
|
63 |
|
64 |
with gr.Blocks() as visualizer:
|
65 |
-
gr.Markdown("# Result")
|
66 |
gr.Markdown(
|
67 |
-
"The image to the below shows where Dawsonia found text in the image."
|
68 |
)
|
69 |
|
70 |
with gr.Row():
|
@@ -86,7 +87,7 @@ with gr.Blocks() as visualizer:
|
|
86 |
"← Previous", visible=False, interactive=False, scale=0
|
87 |
)
|
88 |
right = gr.Button("Next →", visible=False, scale=0)
|
89 |
-
|
90 |
collection = gr.State()
|
91 |
current_page_index = gr.State(0)
|
92 |
|
@@ -95,7 +96,7 @@ with gr.Blocks() as visualizer:
|
|
95 |
right.click(
|
96 |
right_button_click, [collection, current_page_index], current_page_index
|
97 |
)
|
98 |
-
|
99 |
# Updates on collection change:
|
100 |
# - update the view
|
101 |
# - reset the page index (always start on page 0)
|
|
|
26 |
|
27 |
Collection: TypeAlias = list[Page]
|
28 |
|
29 |
+
|
30 |
def render_image(collection: Collection, current_page_index: int) -> str:
|
31 |
return _IMAGE_TEMPLATE.render(
|
32 |
page=collection[current_page_index],
|
33 |
)
|
34 |
|
35 |
+
|
36 |
def toggle_navigation_button(collection: Collection):
|
37 |
visible = len(collection) > 1
|
38 |
return gr.update(visible=visible)
|
|
|
64 |
|
65 |
|
66 |
with gr.Blocks() as visualizer:
|
|
|
67 |
gr.Markdown(
|
68 |
+
"🛈 The image to the below shows where Dawsonia found text in the image."
|
69 |
)
|
70 |
|
71 |
with gr.Row():
|
|
|
87 |
"← Previous", visible=False, interactive=False, scale=0
|
88 |
)
|
89 |
right = gr.Button("Next →", visible=False, scale=0)
|
90 |
+
|
91 |
collection = gr.State()
|
92 |
current_page_index = gr.State(0)
|
93 |
|
|
|
96 |
right.click(
|
97 |
right_button_click, [collection, current_page_index], current_page_index
|
98 |
)
|
99 |
+
|
100 |
# Updates on collection change:
|
101 |
# - update the view
|
102 |
# - reset the page index (always start on page 0)
|