Duplicate from sussahoo/table_extraction

Co-authored-by: Susanta Sahoo <[email protected]>

.gitattributes

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+*.7z filter=lfs diff=lfs merge=lfs -text
+*.arrow filter=lfs diff=lfs merge=lfs -text
+*.bin filter=lfs diff=lfs merge=lfs -text
+*.bz2 filter=lfs diff=lfs merge=lfs -text
+*.ckpt filter=lfs diff=lfs merge=lfs -text
+*.ftz filter=lfs diff=lfs merge=lfs -text
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+*.joblib filter=lfs diff=lfs merge=lfs -text
+*.lfs.* filter=lfs diff=lfs merge=lfs -text
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+*.model filter=lfs diff=lfs merge=lfs -text
+*.msgpack filter=lfs diff=lfs merge=lfs -text
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+*.pickle filter=lfs diff=lfs merge=lfs -text
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+*.pt filter=lfs diff=lfs merge=lfs -text
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+*tfevents* filter=lfs diff=lfs merge=lfs -text

README.md

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+---
+title: Table Extraction
+emoji: 💻
+colorFrom: pink
+colorTo: purple
+sdk: gradio
+sdk_version: 3.13.0
+app_file: app.py
+pinned: false
+duplicated_from: sussahoo/table_extraction
+---
+
+Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference

app.py

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+from PIL import Image, ImageEnhance, ImageOps
+import string
+from collections import Counter
+from itertools import tee, count
+import pytesseract
+from pytesseract import Output
+import json
+import pandas as pd
+
+# import matplotlib.pyplot as plt
+import cv2
+import numpy as np
+from transformers import DetrFeatureExtractor
+from transformers import TableTransformerForObjectDetection
+import torch
+import gradio as gr
+import pdf2image
+
+
+def plot_results_detection(
+    model, image, prob, bboxes_scaled, delta_xmin, delta_ymin, delta_xmax, delta_ymax
+):
+    plt.imshow(image)
+    ax = plt.gca()
+
+    for p, (xmin, ymin, xmax, ymax) in zip(prob, bboxes_scaled.tolist()):
+        cl = p.argmax()
+        xmin, ymin, xmax, ymax = (
+            xmin - delta_xmin,
+            ymin - delta_ymin,
+            xmax + delta_xmax,
+            ymax + delta_ymax,
+        )
+        ax.add_patch(
+            plt.Rectangle(
+                (xmin, ymin),
+                xmax - xmin,
+                ymax - ymin,
+                fill=False,
+                color="red",
+                linewidth=3,
+            )
+        )
+        text = f"{model.config.id2label[cl.item()]}: {p[cl]:0.2f}"
+        ax.text(
+            xmin - 20,
+            ymin - 50,
+            text,
+            fontsize=10,
+            bbox=dict(facecolor="yellow", alpha=0.5),
+        )
+    plt.axis("off")
+
+
+def crop_tables(pil_img, prob, boxes, delta_xmin, delta_ymin, delta_xmax, delta_ymax):
+    """
+    crop_tables and plot_results_detection must have same co-ord shifts because 1 only plots the other one updates co-ordinates
+    """
+    cropped_img_list = []
+
+    for p, (xmin, ymin, xmax, ymax) in zip(prob, boxes.tolist()):
+
+        xmin, ymin, xmax, ymax = (
+            xmin - delta_xmin,
+            ymin - delta_ymin,
+            xmax + delta_xmax,
+            ymax + delta_ymax,
+        )
+        cropped_img = pil_img.crop((xmin, ymin, xmax, ymax))
+        cropped_img_list.append(cropped_img)
+    return cropped_img_list
+
+
+def add_padding(pil_img, top, right, bottom, left, color=(255, 255, 255)):
+    """
+    Image padding as part of TSR pre-processing to prevent missing table edges
+    """
+    width, height = pil_img.size
+    new_width = width + right + left
+    new_height = height + top + bottom
+    result = Image.new(pil_img.mode, (new_width, new_height), color)
+    result.paste(pil_img, (left, top))
+    return result
+
+
+def table_detector(image, THRESHOLD_PROBA):
+    """
+    Table detection using DEtect-object TRansformer pre-trained on 1 million tables
+    """
+
+    feature_extractor = DetrFeatureExtractor(do_resize=True, size=800, max_size=800)
+    encoding = feature_extractor(image, return_tensors="pt")
+
+    model = TableTransformerForObjectDetection.from_pretrained(
+        "microsoft/table-transformer-detection"
+    )
+
+    with torch.no_grad():
+        outputs = model(**encoding)
+
+    probas = outputs.logits.softmax(-1)[0, :, :-1]
+    keep = probas.max(-1).values > THRESHOLD_PROBA
+
+    target_sizes = torch.tensor(image.size[::-1]).unsqueeze(0)
+    postprocessed_outputs = feature_extractor.post_process(outputs, target_sizes)
+    bboxes_scaled = postprocessed_outputs[0]["boxes"][keep]
+
+    return (model, probas[keep], bboxes_scaled)
+
+
+def table_struct_recog(image, THRESHOLD_PROBA):
+    """
+    Table structure recognition using DEtect-object TRansformer pre-trained on 1 million tables
+    """
+
+    feature_extractor = DetrFeatureExtractor(do_resize=True, size=1000, max_size=1000)
+    encoding = feature_extractor(image, return_tensors="pt")
+
+    model = TableTransformerForObjectDetection.from_pretrained(
+        "microsoft/table-transformer-structure-recognition"
+    )
+    with torch.no_grad():
+        outputs = model(**encoding)
+
+    probas = outputs.logits.softmax(-1)[0, :, :-1]
+    keep = probas.max(-1).values > THRESHOLD_PROBA
+
+    target_sizes = torch.tensor(image.size[::-1]).unsqueeze(0)
+    postprocessed_outputs = feature_extractor.post_process(outputs, target_sizes)
+    bboxes_scaled = postprocessed_outputs[0]["boxes"][keep]
+
+    return (model, probas[keep], bboxes_scaled)
+
+
+def generate_structure(
+    model, pil_img, prob, boxes, expand_rowcol_bbox_top, expand_rowcol_bbox_bottom
+):
+    colors = ["red", "blue", "green", "yellow", "orange", "violet"]
+    """
+    Co-ordinates are adjusted here by 3 'pixels'
+    To plot table pillow image and the TSR bounding boxes on the table
+    """
+    # plt.figure(figsize=(32,20))
+    # plt.imshow(pil_img)
+    # ax = plt.gca()
+    rows = {}
+    cols = {}
+    idx = 0
+    for p, (xmin, ymin, xmax, ymax) in zip(prob, boxes.tolist()):
+
+        xmin, ymin, xmax, ymax = xmin, ymin, xmax, ymax
+        cl = p.argmax()
+        class_text = model.config.id2label[cl.item()]
+        text = f"{class_text}: {p[cl]:0.2f}"
+        # or (class_text == 'table column')
+        # if (class_text == 'table row')  or (class_text =='table projected row header') or (class_text == 'table column'):
+        # ax.add_patch(plt.Rectangle((xmin, ymin), xmax - xmin, ymax - ymin,fill=False, color=colors[0], linewidth=2))
+        # ax.text(xmin-10, ymin-10, text, fontsize=5, bbox=dict(facecolor='yellow', alpha=0.5))
+
+        if class_text == "table row":
+            rows["table row." + str(idx)] = (
+                xmin,
+                ymin - expand_rowcol_bbox_top,
+                xmax,
+                ymax + expand_rowcol_bbox_bottom,
+            )
+        if class_text == "table column":
+            cols["table column." + str(idx)] = (
+                xmin,
+                ymin - expand_rowcol_bbox_top,
+                xmax,
+                ymax + expand_rowcol_bbox_bottom,
+            )
+
+        idx += 1
+
+    # plt.axis('on')
+    return rows, cols
+
+
+def sort_table_featuresv2(rows: dict, cols: dict):
+    # Sometimes the header and first row overlap, and we need the header bbox not to have first row's bbox inside the headers bbox
+    rows_ = {
+        table_feature: (xmin, ymin, xmax, ymax)
+        for table_feature, (xmin, ymin, xmax, ymax) in sorted(
+            rows.items(), key=lambda tup: tup[1][1]
+        )
+    }
+    cols_ = {
+        table_feature: (xmin, ymin, xmax, ymax)
+        for table_feature, (xmin, ymin, xmax, ymax) in sorted(
+            cols.items(), key=lambda tup: tup[1][0]
+        )
+    }
+
+    return rows_, cols_
+
+
+def individual_table_featuresv2(pil_img, rows: dict, cols: dict):
+
+    for k, v in rows.items():
+        xmin, ymin, xmax, ymax = v
+        cropped_img = pil_img.crop((xmin, ymin, xmax, ymax))
+        rows[k] = xmin, ymin, xmax, ymax, cropped_img
+
+    for k, v in cols.items():
+        xmin, ymin, xmax, ymax = v
+        cropped_img = pil_img.crop((xmin, ymin, xmax, ymax))
+        cols[k] = xmin, ymin, xmax, ymax, cropped_img
+
+    return rows, cols
+
+
+def object_to_cellsv2(
+    master_row: dict,
+    cols: dict,
+    expand_rowcol_bbox_top,
+    expand_rowcol_bbox_bottom,
+    padd_left,
+):
+    """Removes redundant bbox for rows&columns and divides each row into cells from columns
+    Args:
+    Returns:
+
+    """
+    cells_img = {}
+    header_idx = 0
+    row_idx = 0
+    previous_xmax_col = 0
+    new_cols = {}
+    new_master_row = {}
+    previous_ymin_row = 0
+    new_cols = cols
+    new_master_row = master_row
+    ## Below 2 for loops remove redundant bounding boxes ###
+    # for k_col, v_col in cols.items():
+    #     xmin_col, _, xmax_col, _, col_img = v_col
+    #     if (np.isclose(previous_xmax_col, xmax_col, atol=5)) or (xmin_col >= xmax_col):
+    #         print('Found a column with double bbox')
+    #         continue
+    #     previous_xmax_col = xmax_col
+    #     new_cols[k_col] = v_col
+
+    # for k_row, v_row in master_row.items():
+    #     _, ymin_row, _, ymax_row, row_img = v_row
+    #     if (np.isclose(previous_ymin_row, ymin_row, atol=5)) or (ymin_row >= ymax_row):
+    #         print('Found a row with double bbox')
+    #         continue
+    #     previous_ymin_row = ymin_row
+    #     new_master_row[k_row] = v_row
+    ######################################################
+    for k_row, v_row in new_master_row.items():
+
+        _, _, _, _, row_img = v_row
+        xmax, ymax = row_img.size
+        xa, ya, xb, yb = 0, 0, 0, ymax
+        row_img_list = []
+        # plt.imshow(row_img)
+        # st.pyplot()
+        for idx, kv in enumerate(new_cols.items()):
+            k_col, v_col = kv
+            xmin_col, _, xmax_col, _, col_img = v_col
+            xmin_col, xmax_col = xmin_col - padd_left - 10, xmax_col - padd_left
+            # plt.imshow(col_img)
+            # st.pyplot()
+            # xa + 3 : to remove borders on the left side of the cropped cell
+            # yb = 3: to remove row information from the above row of the cropped cell
+            # xb - 3: to remove borders on the right side of the cropped cell
+            xa = xmin_col
+            xb = xmax_col
+            if idx == 0:
+                xa = 0
+            if idx == len(new_cols) - 1:
+                xb = xmax
+            xa, ya, xb, yb = xa, ya, xb, yb
+
+            row_img_cropped = row_img.crop((xa, ya, xb, yb))
+            row_img_list.append(row_img_cropped)
+
+        cells_img[k_row + "." + str(row_idx)] = row_img_list
+        row_idx += 1
+
+    return cells_img, len(new_cols), len(new_master_row) - 1
+
+
+def pytess(cell_pil_img):
+    return " ".join(
+        pytesseract.image_to_data(
+            cell_pil_img,
+            output_type=Output.DICT,
+            config="-c tessedit_char_blacklist=œ˜â€œï¬â™Ã©œ¢!|”?«“¥ --psm 6 preserve_interword_spaces",
+        )["text"]
+    ).strip()
+
+
+def uniquify(seq, suffs=count(1)):
+    """Make all the items unique by adding a suffix (1, 2, etc).
+    Credit: https://stackoverflow.com/questions/30650474/python-rename-duplicates-in-list-with-progressive-numbers-without-sorting-list
+    `seq` is mutable sequence of strings.
+    `suffs` is an optional alternative suffix iterable.
+    """
+    not_unique = [k for k, v in Counter(seq).items() if v > 1]
+
+    suff_gens = dict(zip(not_unique, tee(suffs, len(not_unique))))
+    for idx, s in enumerate(seq):
+        try:
+            suffix = str(next(suff_gens[s]))
+        except KeyError:
+            continue
+        else:
+            seq[idx] += suffix
+
+    return seq
+
+
+def clean_dataframe(df):
+    """
+    Remove irrelevant symbols that appear with tesseractOCR
+    """
+    # df.columns = [col.replace('|', '') for col in df.columns]
+
+    for col in df.columns:
+
+        df[col] = df[col].str.replace("'", "", regex=True)
+        df[col] = df[col].str.replace('"', "", regex=True)
+        df[col] = df[col].str.replace("]", "", regex=True)
+        df[col] = df[col].str.replace("[", "", regex=True)
+        df[col] = df[col].str.replace("{", "", regex=True)
+        df[col] = df[col].str.replace("}", "", regex=True)
+        df[col] = df[col].str.replace("|", "", regex=True)
+    return df
+
+
+def create_dataframe(cells_pytess_result: list, max_cols: int, max_rows: int, csv_path):
+    """Create dataframe using list of cell values of the table, also checks for valid header of dataframe
+    Args:
+        cells_pytess_result: list of strings, each element representing a cell in a table
+        max_cols, max_rows: number of columns and rows
+    Returns:
+        dataframe : final dataframe after all pre-processing
+    """
+
+    headers = cells_pytess_result[:max_cols]
+    new_headers = uniquify(headers, (f" {x!s}" for x in string.ascii_lowercase))
+    counter = 0
+
+    cells_list = cells_pytess_result[max_cols:]
+    df = pd.DataFrame("", index=range(0, max_rows), columns=new_headers)
+
+    cell_idx = 0
+    for nrows in range(max_rows):
+        for ncols in range(max_cols):
+            df.iat[nrows, ncols] = str(cells_list[cell_idx])
+            cell_idx += 1
+
+    ## To check if there are duplicate headers if result of uniquify+col == col
+    ## This check removes headers when all headers are empty or if median of header word count is less than 6
+    for x, col in zip(string.ascii_lowercase, new_headers):
+        if f" {x!s}" == col:
+            counter += 1
+    header_char_count = [len(col) for col in new_headers]
+
+    # if (counter == len(new_headers)) or (statistics.median(header_char_count) < 6):
+    #     st.write('woooot')
+    #     df.columns = uniquify(df.iloc[0], (f' {x!s}' for x in string.ascii_lowercase))
+    #     df = df.iloc[1:,:]
+
+    df = clean_dataframe(df)
+    # df.to_csv(csv_path)
+
+    return df
+
+def postprocess_dataframes(result_tables):
+    """
+    Normalize column names
+    """
+    # df.columns = [col.replace('|', '') for col in df.columns]
+    res = {}
+    for idx, table_df in enumerate(result_tables):
+        result_df = pd.DataFrame()
+        for col in table_df.columns:
+            if col.lower().startswith("item"):
+                result_df["name"] = table_df[col].copy()
+            if (
+                col.lower().startswith("total")
+                or col.lower().startswith("amount")
+                or col.lower().startswith("cost")
+            ):
+                result_df["amount"] = table_df[col].copy()
+        print(result_df.columns)
+        if len(result_df.columns) == 0:
+            result_df["name"] = table_df.iloc[:, 0].copy()
+            result_df["amount"] = table_df.iloc[:, 1].copy()
+
+        result_df["cost_code"] = ""
+        res["Table1" + str(idx)] = result_df.to_json(orient="records")
+    return res
+
+
+def process_image(image):
+    # if pdf:
+    #     path_to_pdf = pdf.name
+    #     # convert PDF to PIL images (one image by page)
+    #     first_page=True # we want here only the first page as image
+    #     if first_page: last_page = 1
+    #     else: last_page = None
+    #     imgs = pdf2image.convert_from_path(path_to_pdf, last_page=last_page)
+    #     image = imgs[0]
+    TD_THRESHOLD = 0.7
+    TSR_THRESHOLD = 0.8
+    padd_top = 100
+    padd_left = 100
+    padd_bottom = 100
+    padd_right = 20
+    delta_xmin = 0
+    delta_ymin = 0
+    delta_xmax = 0
+    delta_ymax = 0
+    expand_rowcol_bbox_top = 0
+    expand_rowcol_bbox_bottom = 0
+
+    image = image.convert("RGB")
+    model, probas, bboxes_scaled = table_detector(image, THRESHOLD_PROBA=TD_THRESHOLD)
+    # plot_results_detection(model, image, probas, bboxes_scaled,  delta_xmin, delta_ymin, delta_xmax, delta_ymax)
+    cropped_img_list = crop_tables(
+        image, probas, bboxes_scaled, delta_xmin, delta_ymin, delta_xmax, delta_ymax
+    )
+
+    result = []
+    for idx, unpadded_table in enumerate(cropped_img_list):
+        table = add_padding(
+            unpadded_table, padd_top, padd_right, padd_bottom, padd_left
+        )
+        model, probas, bboxes_scaled = table_struct_recog(
+            table, THRESHOLD_PROBA=TSR_THRESHOLD
+        )
+        rows, cols = generate_structure(
+            model,
+            table,
+            probas,
+            bboxes_scaled,
+            expand_rowcol_bbox_top,
+            expand_rowcol_bbox_bottom,
+        )
+        rows, cols = sort_table_featuresv2(rows, cols)
+        master_row, cols = individual_table_featuresv2(table, rows, cols)
+        cells_img, max_cols, max_rows = object_to_cellsv2(
+            master_row,
+            cols,
+            expand_rowcol_bbox_top,
+            expand_rowcol_bbox_bottom,
+            padd_left,
+        )
+        sequential_cell_img_list = []
+        for k, img_list in cells_img.items():
+            for img in img_list:
+                sequential_cell_img_list.append(pytess(img))
+
+        csv_path = "/content/sample_data/table_" + str(idx)
+        df = create_dataframe(sequential_cell_img_list, max_cols, max_rows, csv_path)
+        result.append(df)
+    output = postprocess_dataframes(result)
+    return output
+
+
+title = "Interactive demo OCR: microsoft - table-transformer-detection + tesseract"
+description = "Demo for microsoft - table-transformer-detection + tesseract"
+article = "<p style='text-align: center'></p>"
+examples = [["image_0.png"]]
+
+iface = gr.Interface(
+    fn=process_image,
+    inputs=gr.Image(type="pil"),
+    outputs="text",
+    title=title,
+    description=description,
+    article=article,
+    examples=examples,
+)
+iface.launch(debug=False)

packages.txt

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+tesseract-ocr
+poppler-utils

requirements.txt

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+opencv-python
+pytesseract
+Pillow
+gradio
+timm
+transformers
+numpy
+pandas
+torch
+craft_text_detector
+transformers[sentencepiece]
+pdf2image