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app.py

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+import streamlit as st
+from PIL import Image, ImageEnhance
+import statistics
+import os
+import string
+from collections import Counter 
+from itertools import tee, count
+# import TDTSR
+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 TrOCRProcessor, VisionEncoderDecoderModel
+# from cv2 import dnn_superres
+from transformers import DetrFeatureExtractor
+from transformers import DetrForObjectDetection
+import torch
+import asyncio
+# pytesseract.pytesseract.tesseract_cmd = r'C:\Program Files\Tesseract-OCR\tesseract.exe'
+
+
+st.set_option('deprecation.showPyplotGlobalUse', False)
+st.set_page_config(layout='wide')
+st.title("Table Detection and Table Structure Recognition")
+st.write("Implemented by MSFT team: https://github.com/microsoft/table-transformer")
+
+
+def PIL_to_cv(pil_img):
+    return cv2.cvtColor(np.array(pil_img), cv2.COLOR_RGB2BGR) 
+
+def cv_to_PIL(cv_img):
+    return Image.fromarray(cv2.cvtColor(cv_img, cv2.COLOR_BGR2RGB))
+
+
+async 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 super_res(pil_img):
+    # '''
+    # Useful for low-res docs
+    # '''
+    # requires opencv-contrib-python installed without the opencv-python
+    # sr = dnn_superres.DnnSuperResImpl_create()
+    # image = PIL_to_cv(pil_img)
+    # model_path = "/data/Salman/TRD/code/table-transformer/transformers/LapSRN_x2.pb"
+    # model_name = 'lapsrn'
+    # model_scale = 2
+    # sr.readModel(model_path)
+    # sr.setModel(model_name, model_scale)
+    # final_img = sr.upsample(image)
+    # final_img = cv_to_PIL(final_img)
+
+    # return final_img
+
+
+def sharpen_image(pil_img):
+
+    img = PIL_to_cv(pil_img)
+    sharpen_kernel = np.array([[-1, -1, -1], 
+                               [-1,  9, -1], 
+                               [-1, -1, -1]])
+
+    sharpen = cv2.filter2D(img, -1, sharpen_kernel)
+    pil_img = cv_to_PIL(sharpen)
+    return pil_img
+
+
+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 binarizeBlur_image(pil_img):
+    image = PIL_to_cv(pil_img)
+    thresh = cv2.threshold(image, 150, 255, cv2.THRESH_BINARY_INV)[1]
+
+    result = cv2.GaussianBlur(thresh, (5,5), 0)
+    result = 255 - result
+    return cv_to_PIL(result)
+
+
+
+def td_postprocess(pil_img):
+    '''
+    Removes gray background from tables
+    '''
+    img = PIL_to_cv(pil_img)
+
+    hsv = cv2.cvtColor(img, cv2.COLOR_BGR2HSV)
+    mask = cv2.inRange(hsv, (0, 0, 100), (255, 5, 255)) # (0, 0, 100), (255, 5, 255)
+    nzmask = cv2.inRange(hsv, (0, 0, 5), (255, 255, 255)) # (0, 0, 5), (255, 255, 255))
+    nzmask = cv2.erode(nzmask, np.ones((3,3))) # (3,3)
+    mask = mask & nzmask
+
+    new_img = img.copy()
+    new_img[np.where(mask)] = 255
+
+
+    return cv_to_PIL(new_img)
+
+# def super_res(pil_img):
+#     # requires opencv-contrib-python installed without the opencv-python
+#     sr = dnn_superres.DnnSuperResImpl_create()
+#     image = PIL_to_cv(pil_img)
+#     model_path = "./LapSRN_x8.pb"
+#     model_name = model_path.split('/')[1].split('_')[0].lower()
+#     model_scale = int(model_path.split('/')[1].split('_')[1].split('.')[0][1])
+
+#     sr.readModel(model_path)
+#     sr.setModel(model_name, model_scale)
+#     final_img = sr.upsample(image)
+#     final_img = cv_to_PIL(final_img)
+
+#     return final_img
+
+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 = DetrForObjectDetection.from_pretrained("SalML/DETR-table-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 = DetrForObjectDetection.from_pretrained("SalML/DETR-table-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)
+
+
+
+
+
+class TableExtractionPipeline():
+
+    colors = ["red", "blue", "green", "yellow", "orange", "violet"]
+
+    # colors = ["red", "blue", "green", "red", "red", "red"]
+
+    def add_padding(self, 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 plot_results_detection(self, c1, model, 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 
+        '''
+        # st.write('img_obj')
+        # st.write(pil_img)
+        plt.imshow(pil_img)
+        ax = plt.gca()
+
+        for p, (xmin, ymin, xmax, ymax) in zip(prob, boxes.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')
+        c1.pyplot()
+
+
+    def crop_tables(self, 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 generate_structure(self, c2, model, pil_img, prob, boxes, expand_rowcol_bbox_top, expand_rowcol_bbox_bottom):
+        '''
+        Co-ordinates are adjusted here by 3 'pixels'
+        To plot table pillow image and the TSR bounding boxes on the table
+        '''
+        # st.write('img_obj')
+        # st.write(pil_img)
+        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=self.colors[cl.item()], 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')
+        c2.pyplot()
+        return rows, cols
+
+    def sort_table_featuresv2(self, 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(self, 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(self, 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 clean_dataframe(self, 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)
+        return df
+
+    @st.cache
+    def convert_df(self, df):
+        return df.to_csv().encode('utf-8')
+
+
+    def create_dataframe(self, c3, cells_pytess_result:list, max_cols:int, max_rows:int):
+        '''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 = self.clean_dataframe(df)
+        
+        c3.dataframe(df)
+        csv = self.convert_df(df)
+        c3.download_button("Download table", csv, "file.csv", "text/csv", key='download-csv')
+        
+        return df
+
+
+
+
+
+
+    async def start_process(self, image_path:str, TD_THRESHOLD, TSR_THRESHOLD, padd_top, padd_left, padd_bottom, padd_right, delta_xmin, delta_ymin, delta_xmax, delta_ymax, expand_rowcol_bbox_top, expand_rowcol_bbox_bottom):
+        '''
+        Initiates process of generating pandas dataframes from raw pdf-page images
+        '''
+        image = Image.open(image_path).convert("RGB")
+        model, probas, bboxes_scaled = table_detector(image, THRESHOLD_PROBA=TD_THRESHOLD)
+
+        if bboxes_scaled.nelement() == 0:
+            print('No table found in the pdf-page image'+image_path.split('/')[-1])
+            return ''
+        
+        # try:
+        # st.write('Document: '+image_path.split('/')[-1])
+        c1, c2, c3 = st.columns((1,1,1))
+
+        self.plot_results_detection(c1, model, image, probas, bboxes_scaled,  delta_xmin, delta_ymin, delta_xmax, delta_ymax) 
+        cropped_img_list = self.crop_tables(image, probas, bboxes_scaled, delta_xmin, delta_ymin, delta_xmax, delta_ymax)
+
+        for unpadded_table in cropped_img_list:
+
+            table = self.add_padding(unpadded_table, padd_top, padd_right, padd_bottom, padd_left)
+            # table = super_res(table)
+            # table = binarizeBlur_image(table)
+            # table = sharpen_image(table) # Test sharpen image next
+            # table = td_postprocess(table)
+
+            model, probas, bboxes_scaled = table_struct_recog(table, THRESHOLD_PROBA=TSR_THRESHOLD)
+            rows, cols = self.generate_structure(c2, model, table, probas, bboxes_scaled, expand_rowcol_bbox_top, expand_rowcol_bbox_bottom)
+            # st.write(len(rows), len(cols))
+            rows, cols = self.sort_table_featuresv2(rows, cols)
+            master_row, cols = self.individual_table_featuresv2(table, rows, cols)
+
+            cells_img, max_cols, max_rows = self.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:
+                    # img = super_res(img)
+                    # img = sharpen_image(img) # Test sharpen image next
+                    # img = binarizeBlur_image(img)
+                    # img = self.add_padding(img, 10,10,10,10)
+                    # plt.imshow(img)
+                    # c3.pyplot()
+                    sequential_cell_img_list.append(pytess(img))
+
+            cells_pytess_result = await asyncio.gather(*sequential_cell_img_list)
+            
+
+            self.create_dataframe(c3, cells_pytess_result, max_cols, max_rows)
+            st.write('Errors in OCR is due to either quality of the image or performance of the OCR')
+        # except:
+        #     st.write('Either incorrectly identified table or no table, to debug remove try/except')
+            # break
+        # break
+
+
+
+
+if __name__ == "__main__":
+
+    img_name = st.file_uploader("Upload an image with table(s)")
+
+    padd_top = st.slider('Padding top', 0, 200, 20)
+    padd_left = st.slider('Padding left', 0, 200, 20)
+    padd_right = st.slider('Padding right', 0, 200, 20)
+    padd_bottom = st.slider('Padding bottom', 0, 200, 20)
+
+
+    te = TableExtractionPipeline()
+    # for img in image_list:
+    if img_name is not None:
+        asyncio.run(te.start_process(img_name, TD_THRESHOLD=0.6, TSR_THRESHOLD=0.8, padd_top=padd_top, padd_left=padd_left, padd_bottom=padd_bottom, padd_right=padd_right, delta_xmin=0, delta_ymin=0, delta_xmax=0, delta_ymax=0, expand_rowcol_bbox_top=0, expand_rowcol_bbox_bottom=0))
+
+
+

packages.txt

@@ -0,0 +1,6 @@
+ffmpeg 
+libsm6 
+libxext6 
+libgl1
+tesseract-ocr-eng
+python3-opencv

requirements.txt

@@ -0,0 +1,46 @@
+Cython==0.29.14
+dask==2021.3.1
+datasets==1.18.3
+Flask==2.0.1
+GitPython==3.1.26
+imutils==0.5.4
+multiprocess==0.70.12.2
+numba==0.54.1
+numexpr==2.7.3
+numpy==1.20.3
+oauthlib==3.1.0
+opencv-contrib-python==4.6.0.66
+openpyxl==3.0.7
+Pillow==9.0.1
+plotly==4.14.3
+ply==3.11
+protobuf==3.14.0
+psutil==5.8.0
+pyarrow==7.0.0
+pydantic==1.7.3
+pydeck==0.7.1
+PyDictionary==2.0.1
+pydot==1.4.2
+pymongo==4.0.2
+Pympler==1.0.1
+PyMuPDF==1.20.2
+pyperclip==1.8.2
+pyppeteer==0.2.5
+pyquery==1.4.3
+pyreadline3==3.3
+pytesseract==0.3.10
+pytz-deprecation-shim==0.1.0.post0
+PyWavelets==1.1.1
+PyYAML==5.4.1
+scipy==1.4.1
+seaborn==0.11.1
+sklearn==0.0
+streamlit==1.5.1
+timm==0.6.7
+tokenizers==0.12.1
+toml==0.10.2
+toolz==0.11.1
+torch==1.10.0
+torchvision==0.11.1
+-e git+https://github.com/nielsrogge/transformers.git@d34f7e6ffbb911d39465173ef2b35ba147ef58a9#egg=transformers
+urllib3==1.26.7