# PDF Parsing

## Table of Contents

- 1. Overview
  - 1.1. Requirements
    - 1.1.1. Python packages
    - 1.1.2. External
  - 1.2. Contributing
  - 1.3. Example usage
  - 1.4. Possible improvements
- 2. Preparing data
  - 2.1. Converting PDFs to images
  - 2.2. Detecting image orientation and applying rotation.
- 3. Detecting tables
  - 3.1. Improving accuracy
- 4. OCR tables
  - 4.1. Training Tesseract
  - 4.2. Blur
  - 4.3. Threshold
  - 4.4. Finding the vertical and horizontal lines of the table
  - 4.5. Finding the contours
  - 4.6. Sorting the bounding rectangles
  - 4.7. Cropping each cell to the text
  - 4.8. OCR each cell
- 5. Files
  - 5.1. setup.py
  - 5.2. table_ocr
    - 5.2.1. table_ocr/__init__.py
    - 5.2.2. table_ocr/util.py
    - 5.2.3. table_ocr/pdf_to_images/
      - 5.2.3.1. table_ocr/pdf_to_images/__init__.py
      - 5.2.3.2. table_ocr/pdf_to_images/__main__.py
    - 5.2.4. table_ocr/extract_tables/
      - 5.2.4.1. table_ocr/extract_tables/__init__.py
      - 5.2.4.2. table_ocr/extract_tables/__main__.py
    - 5.2.5. table_ocr/extract_cells/
      - 5.2.5.1. table_ocr/extract_cells/__init__.py
      - 5.2.5.2. table_ocr/extract_cells/__main__.py
    - 5.2.6. table_ocr/ocr_image/
      - 5.2.6.1. table_ocr/ocr_image/__init__.py
      - 5.2.6.2. table_ocr/ocr_image/__main__.py
    - 5.2.7. table_ocr/ocr_to_csv/
      - 5.2.7.1. table_ocr/ocr_to_csv/__init__.py
      - 5.2.7.2. table_ocr/ocr_to_csv/__main__.py
- 6. Utils
  - 6.1. Logging

## 1 Overview

This Python package provides utilities for extracting tabular data from PDF files and images of tables.

Given an image that contains a table…

Extract the the text into a CSV format…

    PRIZE,ODDS 1 IN:,# OF WINNERS*
    $3,9.09,"282,447"
    $5,16.66,"154,097"
    $7,40.01,"64,169"
    $10,26.67,"96,283"
    $20,100.00,"25,677"
    $30,290.83,"8,829"
    $50,239.66,"10,714"
    $100,919.66,"2,792"
    $500,"6,652.07",386
    "$40,000","855,899.99",3
    1,i223,
    Toa,,
    ,,
    ,,"* Based upon 2,567,700"

The package is split into modules with narrow focuses.

- `pdf_to_images` uses Poppler and ImageMagick to extract images from a PDF.
- `extract_tables` finds and extracts table-looking things from an image.
- `extract_cells` extracts and orders cells from a table.
- `ocr_image` uses Tesseract to turn a OCR the text from an image of a cell.
- `ocr_to_csv` converts into a CSV the directory structure that `ocr_image` outputs.

### 1.1 Requirements

#### 1.1.1 Python packages

- numpy
- opencv-python
- pytesseract

#### 1.1.2 External

- `pdfimages` from Poppler
- Tesseract
- `mogfrify` ImageMagick

### 1.2 Contributing

This package was created in a literate programming style with the help of Babel.

The unfortunate downside is the obscurity of the tooling. It creates a bit of a barrier for contributors who aren’t already familiar with Emacs and Babel.

### 1.3 Example usage

Here is an example of a shell script that uses each module to turn a pdf with a table into CSV output.

Depending on your needs, you may not need all of these steps. If you already have an image of a table, you can jum straight to extracting the cells.

Each piece is its own python module, so you can also simply import the pieces you need into your own python projects and use them as needed.

    #!/bin/sh

    PDF=$1

    python -m table_ocr.pdf_to_images $PDF | grep .png > /tmp/pdf-images.txt
    cat /tmp/pdf-images.txt | xargs -I{} python -m table_ocr.extract_tables {}  | grep table > /tmp/extracted-tables.txt
    cat /tmp/extracted-tables.txt | xargs -I{} python -m table_ocr.extract_cells {} | grep cells > /tmp/extracted-cells.txt
    cat /tmp/extracted-cells.txt | xargs -I{} python -m table_ocr.ocr_image {} --psm 7 -l table-ocr

    for image in $(cat /tmp/extracted-tables.txt); do
        dir=$(dirname $image)
        python -m table_ocr.ocr_to_csv $(find $dir/cells -name "*.txt")
    done

### 1.4 Possible improvements

Detect text with the stroke-width-transform alogoritm. https://zablo.net/blog/post/stroke-width-transform-swt-python/index.html

## 2 Preparing data

Not all pdfs need to be sent through OCR to extract the text content. If you can click and drag to highlight text in the pdf, then the tools in this library probably aren’t necessary.

### 2.1 Converting PDFs to images

This code calls out to pdfimages from Poppler.

    # Wrapper around the Poppler command line utility "pdfimages" and helpers for
    # finding the output files of that command.
    def pdf_to_images(pdf_filepath):
        """
        Turn a pdf into images
        """
        directory, filename = os.path.split(pdf_filepath)
        with working_dir(directory):
            image_filenames = pdfimages(pdf_filepath)

        # Since pdfimages creates a number of files named each for there page number
        # and doesn't return us the list that it created
        return [os.path.join(directory, f) for f in image_filenames]

    def pdfimages(pdf_filepath):
        """
        Uses the `pdfimages` utility from Poppler
        (https://poppler.freedesktop.org/). Creates images out of each page. Images
        are prefixed by their name sans extension and suffixed by their page number.

        This should work up to pdfs with 999 pages since find matching files in dir
        uses 3 digits in its regex.
        """
        directory, filename = os.path.split(pdf_filepath)
        filename_sans_ext = filename.split(".pdf")[0]
        subprocess.run(["pdfimages", "-png", pdf_filepath, filename.split(".pdf")[0]])
        image_filenames = find_matching_files_in_dir(filename_sans_ext, directory)
        logger.debug(
            "Converted {} into files:\n{}".format(pdf_filepath, "\n".join(image_filenames))
        )
        return image_filenames

    def find_matching_files_in_dir(file_prefix, directory):
        files = [
            filename
            for filename in os.listdir(directory)
            if re.match(r"{}-\d{{3}}.*\.png".format(re.escape(file_prefix)), filename)
        ]
        return files

### 2.2 Detecting image orientation and applying rotation.

Tesseract can detect orientation and we can then use ImageMagick’s mogrify to rotate the image.

Here’s an example of the output we get from orientation detection with Tesseract.

    ➜  example/ tesseract --psm 0 example-000.png -
    Page number: 0
    Orientation in degrees: 90
    Rotate: 270
    Orientation confidence: 26.86
    Script: Latin
    Script confidence: 2.44

The following are some helpers to detect orientation of the images that Poppler extracted and, if the images are rotated or skewed, use ImageMagick’s `mogrify` to correct the rotation. This makes OCR more straightforward.

    def preprocess_img(filepath):
        """
        Processing that involves running shell executables,
        like mogrify to rotate.
        """
        rotate = get_rotate(filepath)
        logger.debug("Rotating {} by {}.".format(filepath, rotate))
        mogrify(filepath, rotate)

    def get_rotate(image_filepath):
        output = (
            subprocess.check_output(["tesseract", "--psm", "0", image_filepath, "-"])
            .decode("utf-8")
            .split("\n")
        )
        output = next(l for l in output if "Rotate: " in l)
        output = output.split(": ")[1]
        return output

    def mogrify(image_filepath, rotate):
        subprocess.run(["mogrify", "-rotate", rotate, image_filepath])

## 3 Detecting tables

This answer from opencv.org was heavily referenced while writing the code around table detection: https://answers.opencv.org/question/63847/how-to-extract-tables-from-an-image/.

It’s much easier to OCR a table when the table is the only thing in the image. This code detects tables in an image and returns a list of images of just the tables, no surrounding text or noise.

The blurring, thresholding, and line detection is used here as well as later on for cell extraction. They are good techniques for cleaning an image up in a way that makes things like shape detection more accurate.

    def find_tables(image):
        BLUR_KERNEL_SIZE = (17, 17)
        STD_DEV_X_DIRECTION = 0
        STD_DEV_Y_DIRECTION = 0
        blurred = cv2.GaussianBlur(image, BLUR_KERNEL_SIZE, STD_DEV_X_DIRECTION, STD_DEV_Y_DIRECTION)
        MAX_COLOR_VAL = 255
        BLOCK_SIZE = 15
        SUBTRACT_FROM_MEAN = -2

        img_bin = cv2.adaptiveThreshold(
            ~blurred,
            MAX_COLOR_VAL,
            cv2.ADAPTIVE_THRESH_MEAN_C,
            cv2.THRESH_BINARY,
            BLOCK_SIZE,
            SUBTRACT_FROM_MEAN,
        )
        vertical = horizontal = img_bin.copy()
        SCALE = 5
        image_width, image_height = horizontal.shape
        horizontal_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (int(image_width / SCALE), 1))
        horizontally_opened = cv2.morphologyEx(img_bin, cv2.MORPH_OPEN, horizontal_kernel)
        vertical_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (1, int(image_height / SCALE)))
        vertically_opened = cv2.morphologyEx(img_bin, cv2.MORPH_OPEN, vertical_kernel)

        horizontally_dilated = cv2.dilate(horizontally_opened, cv2.getStructuringElement(cv2.MORPH_RECT, (40, 1)))
        vertically_dilated = cv2.dilate(vertically_opened, cv2.getStructuringElement(cv2.MORPH_RECT, (1, 60)))

        mask = horizontally_dilated + vertically_dilated
        contours, heirarchy = cv2.findContours(
            mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE,
        )

        MIN_TABLE_AREA = 1e5
        contours = [c for c in contours if cv2.contourArea(c) > MIN_TABLE_AREA]
        perimeter_lengths = [cv2.arcLength(c, True) for c in contours]
        epsilons = [0.1 * p for p in perimeter_lengths]
        approx_polys = [cv2.approxPolyDP(c, e, True) for c, e in zip(contours, epsilons)]
        bounding_rects = [cv2.boundingRect(a) for a in approx_polys]

        # The link where a lot of this code was borrowed from recommends an
        # additional step to check the number of "joints" inside this bounding rectangle.
        # A table should have a lot of intersections. We might have a rectangular image
        # here though which would only have 4 intersections, 1 at each corner.
        # Leaving that step as a future TODO if it is ever necessary.
        images = [image[y:y+h, x:x+w] for x, y, w, h in bounding_rects]
        return images

Here is an the an example of the result of the `find_tables` function.

    import cv2

    image_filename = "resources/examples/example-page.png"
    image = cv2.imread(image_filename, cv2.IMREAD_GRAYSCALE)
    image = find_tables(image)[0]
    cv2.imwrite("resources/examples/example-table.png", image)

↓

### 3.1 Improving accuracy

It’s likely that some images will contain tables that aren’t accurately recognized by the code above. The code will then need to be made more robust. But how will we know that changes to the code don’t break the detection of tables that were previously detected?

It might be good to add some type of test suite in the future that contains a spec that matches a pdf with the pages and pixel coordinates of the detected tables. The coordinates would need to have a range. Something like “example-1.pdf, page-2.png, [450:470, 200:210, 800:820, 1270:1290]” where the elements of the list are valid x, y, w, h ranges. So the test will pass if if the x, y, width and height are anywhere in that range.

## 4 OCR tables

Tesseract does not perform well when run on images of tables. It performs best when given a single line of text with no extra noise.

Therefore, our next task is to find and extract the bounding box of each cell in the table. Run tesseract on each cell. Print a comma seperated output.

We’ll start with an image shown at the end of the previous section.

### 4.1 Training Tesseract

It’s a very good idea to train tesseract. Accuracy will improve tremendously.

Clone the tesstrain repo at https://github.com/tesseract-ocr/tesstrain.

Run the `ocr_tables` script on a few pdfs to generate some training data. That script outputs pairs of `.png` and `.gt.txt` files that can be used by tesstrain.

Make sure the `.gt.txt` files contain an accurate recognition of the corresponding image. Since the first few runs will be untrained, you’ll probably need to fix up a few of the text files.

Once they are accurate, move them to a new subdirectory of the tesstrain repo; `tesstrain/data/<model-name>-ground-truth/`.

You’ll also need to clone the `tessdata_best` repo, https://github.com/tesseract-ocr/tessdata_best and the https://github.com/tesseract-ocr/langdata to use as the start of the training model.

I’m actually not sure how much the punctuation and numbers from `langdata` help. I didn’t keep accurate records while playing with the training, I don’t thoroughly understand it, and it’s not profitable for me to explore it at the moment. It worked for my purposes and that has been good enough.

    make training MODEL_NAME=table-ocr START_MODEL=eng TESSDATA=~/src/tessdata_best PUNC_FILE=~/src/langdata/eng/eng.punc NUMBERS_FILE=~/src/langdata/eng/eng.numbers

Once the training is complete, there will be a new file `tesstrain/data/<model-name>.traineddata`. Copy that file to the directory Tesseract searches for models. On my machine, it was `/usr/local/share/tessdata/`.

### 4.2 Blur

Blurring helps to make noise less noisy so that the overall structure of an image is more detectable.

That gray row at the bottom is kind of noisy. If we don’t somehow clean it up, OpenCV will detect all sorts of odd shapes in there and it will throw off our cell detection.

Cleanup can be accomplished with a blur followed by some thresholding.

    BLUR_KERNEL_SIZE = (17, 17)
    STD_DEV_X_DIRECTION = 0
    STD_DEV_Y_DIRECTION = 0
    blurred = cv2.GaussianBlur(image, BLUR_KERNEL_SIZE, STD_DEV_X_DIRECTION, STD_DEV_Y_DIRECTION)

    image = ~cv2.imread("resources/examples/example-table.png", cv2.IMREAD_GRAYSCALE)
    <<blur>>
    cv2.imwrite("resources/examples/example-table-blurred.png", blurred)

### 4.3 Threshold

We’ve got a bunch of pixels that are gray. Thresholding will turn them all either black or white. Having all black or white pixels lets us do morphological transformations like erosion and dilation.

    MAX_COLOR_VAL = 255
    BLOCK_SIZE = 15
    SUBTRACT_FROM_MEAN = -2

    img_bin = cv2.adaptiveThreshold(
        ~blurred,
        MAX_COLOR_VAL,
        cv2.ADAPTIVE_THRESH_MEAN_C,
        cv2.THRESH_BINARY,
        BLOCK_SIZE,
        SUBTRACT_FROM_MEAN,
    )

    <<threshold>>
    cv2.imwrite("resources/examples/example-table-thresholded.png", img_bin)

### 4.4 Finding the vertical and horizontal lines of the table

    vertical = horizontal = img_bin.copy()
    SCALE = 5
    image_width, image_height = horizontal.shape
    horizontal_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (int(image_width / SCALE), 1))
    horizontally_opened = cv2.morphologyEx(img_bin, cv2.MORPH_OPEN, horizontal_kernel)
    vertical_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (1, int(image_height / SCALE)))
    vertically_opened = cv2.morphologyEx(img_bin, cv2.MORPH_OPEN, vertical_kernel)

    horizontally_dilated = cv2.dilate(horizontally_opened, cv2.getStructuringElement(cv2.MORPH_RECT, (40, 1)))
    vertically_dilated = cv2.dilate(vertically_opened, cv2.getStructuringElement(cv2.MORPH_RECT, (1, 60)))

    mask = horizontally_dilated + vertically_dilated

Note: There’s a wierd issue with the results of the example below when it’s evaluated as part of an export or a full-buffer evaluation. If you evaluate the example by itself, it looks the way it’s intended. If you evaluate it as part of an entire buffer evaluation, like during export, it’s distorted.

    <<lines-of-table>>
    cv2.imwrite("resources/examples/example-table-lines.png", mask)

### 4.5 Finding the contours

Blurring and thresholding allow us to find the lines. Opening the lines allows us to find the contours.

An “Opening” is an erosion followed by a dilation. Great examples and descriptions of each morphological operation can be found at https://docs.opencv.org/trunk/d9/d61/tutorial_py_morphological_ops.html.

> Contours can be explained simply as a curve joining all the continuous points (along the boundary), having same color or intensity. The contours are a useful tool for shape analysis and object detection and recognition.

We can search those contours to find rectangles of certain size.

To do that, we can use OpenCV’s `approxPolyEP` function. It takes as arguments the contour (list of contiguous points), and a number representing how different the polygon perimeter length can be from the true perimeter length of the contour. `0.1` (10%) seems to be a good value. The difference in perimeter length between a 4-sided polygon and a 3-sided polygon is greater than 10% and the difference between a 5+ sided polygon and a 4-sided polygon is less than 10%. So a 4-sided polygon is the polygon with the fewest sides that leaves the difference in perimeter length within our 10% threshold.

Then we just get the bounding rectangle of that polygon and we have our cells!

We might need to do a little more filtering of those rectangles though. We might have accidentally found some noise such as another image on the page or a title header bar or something. If we know our cells are all within a certain size (by area of pixels) then we can filter out the junk cells by removing cells above/below certain sizes.

    contours, heirarchy = cv2.findContours(
        mask, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE,
    )

    perimeter_lengths = [cv2.arcLength(c, True) for c in contours]
    epsilons = [0.05 * p for p in perimeter_lengths]
    approx_polys = [cv2.approxPolyDP(c, e, True) for c, e in zip(contours, epsilons)]

    # Filter out contours that aren't rectangular. Those that aren't rectangular
    # are probably noise.
    approx_rects = [p for p in approx_polys if len(p) == 4]
    bounding_rects = [cv2.boundingRect(a) for a in approx_polys]

    # Filter out rectangles that are too narrow or too short.
    MIN_RECT_WIDTH = 40
    MIN_RECT_HEIGHT = 10
    bounding_rects = [
        r for r in bounding_rects if MIN_RECT_WIDTH < r[2] and MIN_RECT_HEIGHT < r[3]
    ]

    # The largest bounding rectangle is assumed to be the entire table.
    # Remove it from the list. We don't want to accidentally try to OCR
    # the entire table.
    largest_rect = max(bounding_rects, key=lambda r: r[2] * r[3])
    bounding_rects = [b for b in bounding_rects if b is not largest_rect]

    cells = [c for c in bounding_rects]

### 4.6 Sorting the bounding rectangles

We want to process these from left-to-right, top-to-bottom.

I’ve thought of a straightforward algorithm for it, but it could probably be made more efficient.

We’ll find the most rectangle with the most top-left corner. Then we’ll find all of the rectangles that have a center that is within the top-y and bottom-y values of that top-left rectangle. Then we’ll sort those rectangles by the x value of their center. We’ll remove those rectangles from the list and repeat.

    def cell_in_same_row(c1, c2):
        c1_center = c1[1] + c1[3] - c1[3] / 2
        c2_bottom = c2[1] + c2[3]
        c2_top = c2[1]
        return c2_top < c1_center < c2_bottom

    orig_cells = [c for c in cells]
    rows = []
    while cells:
        first = cells[0]
        rest = cells[1:]
        cells_in_same_row = sorted(
            [
                c for c in rest
                if cell_in_same_row(c, first)
            ],
            key=lambda c: c[0]
        )

        row_cells = sorted([first] + cells_in_same_row, key=lambda c: c[0])
        rows.append(row_cells)
        cells = [
            c for c in rest
            if not cell_in_same_row(c, first)
        ]

    # Sort rows by average height of their center.
    def avg_height_of_center(row):
        centers = [y + h - h / 2 for x, y, w, h in row]
        return sum(centers) / len(centers)

    rows.sort(key=avg_height_of_center)

To test if this code works, let’s try sorting the bounding rectangles and numbering them from right to left, top to bottom.

    import cv2
    image = cv2.imread("resources/examples/example-table.png", cv2.IMREAD_GRAYSCALE)
    <<blur>>
    <<threshold>>
    <<lines-of-table>>
    <<bounding-rects>>
    <<sort-contours>>

    FONT_SCALE = 0.7
    FONT_COLOR = (127, 127, 127)
    for i, row in enumerate(rows):
        for j, cell in enumerate(row):
            x, y, w, h = cell
            cv2.putText(
                image,
                "{},{}".format(i, j),
                (int(x + w - w / 2), int(y + h - h / 2)),
                cv2.FONT_HERSHEY_SIMPLEX,
                FONT_SCALE,
                FONT_COLOR,
                2,
            )
    cv2.imwrite("resources/examples/example-table-cells-numbered.png", image)

    def extract_cell_images_from_table(image):
        BLUR_KERNEL_SIZE = (17, 17)
        STD_DEV_X_DIRECTION = 0
        STD_DEV_Y_DIRECTION = 0
        blurred = cv2.GaussianBlur(image, BLUR_KERNEL_SIZE, STD_DEV_X_DIRECTION, STD_DEV_Y_DIRECTION)
        MAX_COLOR_VAL = 255
        BLOCK_SIZE = 15
        SUBTRACT_FROM_MEAN = -2

        img_bin = cv2.adaptiveThreshold(
            ~blurred,
            MAX_COLOR_VAL,
            cv2.ADAPTIVE_THRESH_MEAN_C,
            cv2.THRESH_BINARY,
            BLOCK_SIZE,
            SUBTRACT_FROM_MEAN,
        )
        vertical = horizontal = img_bin.copy()
        SCALE = 5
        image_width, image_height = horizontal.shape
        horizontal_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (int(image_width / SCALE), 1))
        horizontally_opened = cv2.morphologyEx(img_bin, cv2.MORPH_OPEN, horizontal_kernel)
        vertical_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (1, int(image_height / SCALE)))
        vertically_opened = cv2.morphologyEx(img_bin, cv2.MORPH_OPEN, vertical_kernel)

        horizontally_dilated = cv2.dilate(horizontally_opened, cv2.getStructuringElement(cv2.MORPH_RECT, (40, 1)))
        vertically_dilated = cv2.dilate(vertically_opened, cv2.getStructuringElement(cv2.MORPH_RECT, (1, 60)))

        mask = horizontally_dilated + vertically_dilated
        contours, heirarchy = cv2.findContours(
            mask, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE,
        )

        perimeter_lengths = [cv2.arcLength(c, True) for c in contours]
        epsilons = [0.05 * p for p in perimeter_lengths]
        approx_polys = [cv2.approxPolyDP(c, e, True) for c, e in zip(contours, epsilons)]

        # Filter out contours that aren't rectangular. Those that aren't rectangular
        # are probably noise.
        approx_rects = [p for p in approx_polys if len(p) == 4]
        bounding_rects = [cv2.boundingRect(a) for a in approx_polys]

        # Filter out rectangles that are too narrow or too short.
        MIN_RECT_WIDTH = 40
        MIN_RECT_HEIGHT = 10
        bounding_rects = [
            r for r in bounding_rects if MIN_RECT_WIDTH < r[2] and MIN_RECT_HEIGHT < r[3]
        ]

        # The largest bounding rectangle is assumed to be the entire table.
        # Remove it from the list. We don't want to accidentally try to OCR
        # the entire table.
        largest_rect = max(bounding_rects, key=lambda r: r[2] * r[3])
        bounding_rects = [b for b in bounding_rects if b is not largest_rect]

        cells = [c for c in bounding_rects]
        def cell_in_same_row(c1, c2):
            c1_center = c1[1] + c1[3] - c1[3] / 2
            c2_bottom = c2[1] + c2[3]
            c2_top = c2[1]
            return c2_top < c1_center < c2_bottom

        orig_cells = [c for c in cells]
        rows = []
        while cells:
            first = cells[0]
            rest = cells[1:]
            cells_in_same_row = sorted(
                [
                    c for c in rest
                    if cell_in_same_row(c, first)
                ],
                key=lambda c: c[0]
            )

            row_cells = sorted([first] + cells_in_same_row, key=lambda c: c[0])
            rows.append(row_cells)
            cells = [
                c for c in rest
                if not cell_in_same_row(c, first)
            ]

        # Sort rows by average height of their center.
        def avg_height_of_center(row):
            centers = [y + h - h / 2 for x, y, w, h in row]
            return sum(centers) / len(centers)

        rows.sort(key=avg_height_of_center)
        cell_images_rows = []
        for row in rows:
            cell_images_row = []
            for x, y, w, h in row:
                cell_images_row.append(image[y:y+h, x:x+w])
            cell_images_rows.append(cell_images_row)
        return cell_images_rows

    <<extract-cells-from-table>>
    image = cv2.imread("resources/examples/example-table.png", cv2.IMREAD_GRAYSCALE)
    cell_images_rows = extract_cell_images_from_table(image)
    cv2.imwrite("resources/examples/example-table-cell-1-1.png", cell_images_rows[1][1])

### 4.7 Cropping each cell to the text

OCR with Tesseract works best when there is about 10 pixels of white border around the text.

Our bounding rectangles may have picked up some stray pixels from the horizontal and vertical lines of the cells in the table. It’s probobly just a few pixels, much fewer than the width of the text. If that’s the case, then we can remove that noise with a simple open morph.

Once the stray border pixels have been removed, we can expand our border using `copyMakeBorder`.

    def crop_to_text(image):
        MAX_COLOR_VAL = 255
        BLOCK_SIZE = 15
        SUBTRACT_FROM_MEAN = -2

        img_bin = cv2.adaptiveThreshold(
            ~image,
            MAX_COLOR_VAL,
            cv2.ADAPTIVE_THRESH_MEAN_C,
            cv2.THRESH_BINARY,
            BLOCK_SIZE,
            SUBTRACT_FROM_MEAN,
        )

        img_h, img_w = image.shape
        horizontal_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (int(img_w * 0.5), 1))
        vertical_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (1, int(img_h * 0.7)))
        horizontal_lines = cv2.morphologyEx(img_bin, cv2.MORPH_OPEN, horizontal_kernel)
        vertical_lines = cv2.morphologyEx(img_bin, cv2.MORPH_OPEN, vertical_kernel)
        both = horizontal_lines + vertical_lines
        cleaned = img_bin - both

        # Get rid of little noise.
        kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (3, 3))
        opened = cv2.morphologyEx(cleaned, cv2.MORPH_OPEN, kernel)
        opened = cv2.dilate(opened, kernel)

        contours, hierarchy = cv2.findContours(opened, cv2.RETR_LIST, cv2.CHAIN_APPROX_SIMPLE)
        bounding_rects = [cv2.boundingRect(c) for c in contours]
        NUM_PX_COMMA = 6
        MIN_CHAR_AREA = 5 * 9
        char_sized_bounding_rects = [(x, y, w, h) for x, y, w, h in bounding_rects if w * h > MIN_CHAR_AREA]
        if char_sized_bounding_rects:
            minx, miny, maxx, maxy = math.inf, math.inf, 0, 0
            for x, y, w, h in char_sized_bounding_rects:
                minx = min(minx, x)
                miny = min(miny, y)
                maxx = max(maxx, x + w)
                maxy = max(maxy, y + h)
            x, y, w, h = minx, miny, maxx - minx, maxy - miny
            cropped = image[y:min(img_h, y+h+NUM_PX_COMMA), x:min(img_w, x+w)]
        else:
            # If we morphed out all of the text, assume an empty image.
            cropped = MAX_COLOR_VAL * np.ones(shape=(20, 100), dtype=np.uint8)
        bordered = cv2.copyMakeBorder(cropped, 5, 5, 5, 5, cv2.BORDER_CONSTANT, None, 255)
        return bordered

    import cv2
    import numpy as np
    <<crop-to-text>>
    image = cv2.imread("resources/examples/example-table-cell-1-1.png", cv2.IMREAD_GRAYSCALE)
    image = crop_to_text(image)
    cv2.imwrite("resources/examples/example-table-cell-1-1-cropped.png", image)

### 4.8 OCR each cell

If we cleaned up the images well enough, we might get some accurate OCR!

There is plenty that could have gone wrong along the way.

The first step to troubleshooting is to view the intermediate images and see if there’s something about your image that is obviously abnormal, like some really thick noise or a wrongly detected table.

If everything looks reasonable but the OCR is doing something like turning a period into a comma, then you might need to do some custom Tesseract training.

    def ocr_image(image, config):
        return pytesseract.image_to_string(
            image,
            config=config
        )

    import pytesseract
    import cv2
    import numpy as np
    image = cv2.imread("resources/examples/example-table-cell-1-1.png", cv2.IMREAD_GRAYSCALE)
    <<crop-to-text>>
    <<ocr-image>>
    image = crop_to_text(image)
    ocr_image(image, "--psm 7")

    9.09

## 5 Files

### 5.1 setup.py

    import setuptools

    long_description = """
    Utilities for turning images of tables into CSV data. Uses Tesseract and OpenCV.

    Requires binaries for tesseract and pdfimages (from Poppler).
    """
    setuptools.setup(
        name="table_ocr",
        version="0.0.1",
        author="Eric Ihli",
        author_email="eihli@owoga.com",
        description="Turn images of tables into CSV data.",
        long_description=long_description,
        long_description_content_type="text/plain",
        url="https://github.com/eihli/image-table-ocr",
        packages=setuptools.find_packages(),
        classifiers=[
            "Programming Language :: Python :: 3",
            "License :: OSI Approved :: MIT License",
            "Operating System :: OS Independent",
        ],
        install_requires=[
            "pytesseract~=0.3",
            "opencv-python~=4.2",
        ],
        python_requires='>=3.6',
    )

### 5.2 table_ocr

#### 5.2.1 table_ocr/__init__.py

#### 5.2.2 table_ocr/util.py

    from contextlib import contextmanager
    import functools
    import logging
    import os
    import tempfile

    def get_logger(name):
        logger = logging.getLogger(name)
        lvl = os.environ.get("PY_LOG_LVL", "info").upper()
        handler = logging.StreamHandler()
        formatter = logging.Formatter(logging.BASIC_FORMAT)
        handler.setFormatter(formatter)
        logger.addHandler(handler)
        handler.setLevel(lvl)
        logger.setLevel(lvl)
        return logger

    @contextmanager
    def working_dir(directory):
        original_working_dir = os.getcwd()
        try:
            os.chdir(directory)
            yield directory
        finally:
            os.chdir(original_working_dir)

    def make_tempdir(identifier):
        return tempfile.mkdtemp(prefix="{}_".format(identifier))

#### 5.2.3 table_ocr/pdf_to_images/

##### 5.2.3.1 table_ocr/pdf_to_images/__init__.py

    import os
    import re
    import subprocess

    from table_ocr.util import get_logger, working_dir

    logger = get_logger(__name__)

    # Wrapper around the Poppler command line utility "pdfimages" and helpers for
    # finding the output files of that command.
    def pdf_to_images(pdf_filepath):
        """
        Turn a pdf into images
        """
        directory, filename = os.path.split(pdf_filepath)
        with working_dir(directory):
            image_filenames = pdfimages(pdf_filepath)

        # Since pdfimages creates a number of files named each for there page number
        # and doesn't return us the list that it created
        return [os.path.join(directory, f) for f in image_filenames]

    def pdfimages(pdf_filepath):
        """
        Uses the `pdfimages` utility from Poppler
        (https://poppler.freedesktop.org/). Creates images out of each page. Images
        are prefixed by their name sans extension and suffixed by their page number.

        This should work up to pdfs with 999 pages since find matching files in dir
        uses 3 digits in its regex.
        """
        directory, filename = os.path.split(pdf_filepath)
        filename_sans_ext = filename.split(".pdf")[0]
        subprocess.run(["pdfimages", "-png", pdf_filepath, filename.split(".pdf")[0]])
        image_filenames = find_matching_files_in_dir(filename_sans_ext, directory)
        logger.debug(
            "Converted {} into files:\n{}".format(pdf_filepath, "\n".join(image_filenames))
        )
        return image_filenames

    def find_matching_files_in_dir(file_prefix, directory):
        files = [
            filename
            for filename in os.listdir(directory)
            if re.match(r"{}-\d{{3}}.*\.png".format(re.escape(file_prefix)), filename)
        ]
        return files

    def preprocess_img(filepath):
        """
        Processing that involves running shell executables,
        like mogrify to rotate.
        """
        rotate = get_rotate(filepath)
        logger.debug("Rotating {} by {}.".format(filepath, rotate))
        mogrify(filepath, rotate)

    def get_rotate(image_filepath):
        output = (
            subprocess.check_output(["tesseract", "--psm", "0", image_filepath, "-"])
            .decode("utf-8")
            .split("\n")
        )
        output = next(l for l in output if "Rotate: " in l)
        output = output.split(": ")[1]
        return output

    def mogrify(image_filepath, rotate):
        subprocess.run(["mogrify", "-rotate", rotate, image_filepath])

##### 5.2.3.2 table_ocr/pdf_to_images/__main__.py

Takes a variable number of pdf files and creates images out of each page of the file using `pdfimages` from Poppler. Images are created in the same directory that contains the pdf.

Prints each pdf followed by the images extracted from that pdf followed by a blank line.

    python -m table_ocr.prepare_pdfs /tmp/file1/file1.pdf /tmp/file2/file2.pdf ...

    import argparse

    from table_ocr.util import working_dir, make_tempdir, get_logger
    from table_ocr.pdf_to_images import pdf_to_images, preprocess_img

    logger = get_logger(__name__)

    parser = argparse.ArgumentParser()
    parser.add_argument("files", nargs="+")

    def main(files):
        pdf_images = []
        for f in files:
            pdf_images.append((f, pdf_to_images(f)))

        for pdf, images in pdf_images:
            for image in images:
                preprocess_img(image)

        for pdf, images in pdf_images:
            print("{}\n{}\n".format(pdf, "\n".join(images)))

    if __name__ == "__main__":
        args = parser.parse_args()
        main(args.files)

#### 5.2.4 table_ocr/extract_tables/

##### 5.2.4.1 table_ocr/extract_tables/__init__.py

    import cv2

    def find_tables(image):
        BLUR_KERNEL_SIZE = (17, 17)
        STD_DEV_X_DIRECTION = 0
        STD_DEV_Y_DIRECTION = 0
        blurred = cv2.GaussianBlur(image, BLUR_KERNEL_SIZE, STD_DEV_X_DIRECTION, STD_DEV_Y_DIRECTION)
        MAX_COLOR_VAL = 255
        BLOCK_SIZE = 15
        SUBTRACT_FROM_MEAN = -2

        img_bin = cv2.adaptiveThreshold(
            ~blurred,
            MAX_COLOR_VAL,
            cv2.ADAPTIVE_THRESH_MEAN_C,
            cv2.THRESH_BINARY,
            BLOCK_SIZE,
            SUBTRACT_FROM_MEAN,
        )
        vertical = horizontal = img_bin.copy()
        SCALE = 5
        image_width, image_height = horizontal.shape
        horizontal_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (int(image_width / SCALE), 1))
        horizontally_opened = cv2.morphologyEx(img_bin, cv2.MORPH_OPEN, horizontal_kernel)
        vertical_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (1, int(image_height / SCALE)))
        vertically_opened = cv2.morphologyEx(img_bin, cv2.MORPH_OPEN, vertical_kernel)

        horizontally_dilated = cv2.dilate(horizontally_opened, cv2.getStructuringElement(cv2.MORPH_RECT, (40, 1)))
        vertically_dilated = cv2.dilate(vertically_opened, cv2.getStructuringElement(cv2.MORPH_RECT, (1, 60)))

        mask = horizontally_dilated + vertically_dilated
        contours, heirarchy = cv2.findContours(
            mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE,
        )

        MIN_TABLE_AREA = 1e5
        contours = [c for c in contours if cv2.contourArea(c) > MIN_TABLE_AREA]
        perimeter_lengths = [cv2.arcLength(c, True) for c in contours]
        epsilons = [0.1 * p for p in perimeter_lengths]
        approx_polys = [cv2.approxPolyDP(c, e, True) for c, e in zip(contours, epsilons)]
        bounding_rects = [cv2.boundingRect(a) for a in approx_polys]

        # The link where a lot of this code was borrowed from recommends an
        # additional step to check the number of "joints" inside this bounding rectangle.
        # A table should have a lot of intersections. We might have a rectangular image
        # here though which would only have 4 intersections, 1 at each corner.
        # Leaving that step as a future TODO if it is ever necessary.
        images = [image[y:y+h, x:x+w] for x, y, w, h in bounding_rects]
        return images

##### 5.2.4.2 table_ocr/extract_tables/__main__.py

Takes 1 or more image paths as arguments.

Images are opened and read with OpenCV.

Tables are detected and extracted to a new subdirectory of the given image. The subdirectory will be the filename sans the extension. The tables inside that directory will be named `table-000.png`.

If you want to do something with the output, like pipe the paths of the extracted tables into some other utility, here is a description of the output.

For each image path given as an agument, outputs:

1. The given image path
2. Paths of extracted tables; seperated by newlines
3. Empty newline

    import argparse
    import os

    import cv2

    from table_ocr.extract_tables import find_tables

    parser = argparse.ArgumentParser()
    parser.add_argument("files", nargs="+")

    def main(files):
        results = []
        for f in files:
            directory, filename = os.path.split(f)
            image = cv2.imread(f, cv2.IMREAD_GRAYSCALE)
            tables = find_tables(image)
            files = []
            filename_sans_extension = os.path.splitext(filename)[0]
            if tables:
                os.makedirs(os.path.join(directory, filename_sans_extension), exist_ok=True)
            for i, table in enumerate(tables):
                table_filename = "table-{:03d}.png".format(i)
                table_filepath = os.path.join(
                    directory, filename_sans_extension, table_filename
                )
                files.append(table_filepath)
                cv2.imwrite(table_filepath, table)
            if tables:
                results.append((f, files))

        for image_filename, table_filenames in results:
            print("\n".join(table_filenames))

    if __name__ == "__main__":
        args = parser.parse_args()
        files = args.files
        main(files)

#### 5.2.5 table_ocr/extract_cells/

##### 5.2.5.1 table_ocr/extract_cells/__init__.py

    import cv2

    def extract_cell_images_from_table(image):
        BLUR_KERNEL_SIZE = (17, 17)
        STD_DEV_X_DIRECTION = 0
        STD_DEV_Y_DIRECTION = 0
        blurred = cv2.GaussianBlur(image, BLUR_KERNEL_SIZE, STD_DEV_X_DIRECTION, STD_DEV_Y_DIRECTION)
        MAX_COLOR_VAL = 255
        BLOCK_SIZE = 15
        SUBTRACT_FROM_MEAN = -2

        img_bin = cv2.adaptiveThreshold(
            ~blurred,
            MAX_COLOR_VAL,
            cv2.ADAPTIVE_THRESH_MEAN_C,
            cv2.THRESH_BINARY,
            BLOCK_SIZE,
            SUBTRACT_FROM_MEAN,
        )
        vertical = horizontal = img_bin.copy()
        SCALE = 5
        image_width, image_height = horizontal.shape
        horizontal_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (int(image_width / SCALE), 1))
        horizontally_opened = cv2.morphologyEx(img_bin, cv2.MORPH_OPEN, horizontal_kernel)
        vertical_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (1, int(image_height / SCALE)))
        vertically_opened = cv2.morphologyEx(img_bin, cv2.MORPH_OPEN, vertical_kernel)

        horizontally_dilated = cv2.dilate(horizontally_opened, cv2.getStructuringElement(cv2.MORPH_RECT, (40, 1)))
        vertically_dilated = cv2.dilate(vertically_opened, cv2.getStructuringElement(cv2.MORPH_RECT, (1, 60)))

        mask = horizontally_dilated + vertically_dilated
        contours, heirarchy = cv2.findContours(
            mask, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE,
        )

        perimeter_lengths = [cv2.arcLength(c, True) for c in contours]
        epsilons = [0.05 * p for p in perimeter_lengths]
        approx_polys = [cv2.approxPolyDP(c, e, True) for c, e in zip(contours, epsilons)]

        # Filter out contours that aren't rectangular. Those that aren't rectangular
        # are probably noise.
        approx_rects = [p for p in approx_polys if len(p) == 4]
        bounding_rects = [cv2.boundingRect(a) for a in approx_polys]

        # Filter out rectangles that are too narrow or too short.
        MIN_RECT_WIDTH = 40
        MIN_RECT_HEIGHT = 10
        bounding_rects = [
            r for r in bounding_rects if MIN_RECT_WIDTH < r[2] and MIN_RECT_HEIGHT < r[3]
        ]

        # The largest bounding rectangle is assumed to be the entire table.
        # Remove it from the list. We don't want to accidentally try to OCR
        # the entire table.
        largest_rect = max(bounding_rects, key=lambda r: r[2] * r[3])
        bounding_rects = [b for b in bounding_rects if b is not largest_rect]

        cells = [c for c in bounding_rects]
        def cell_in_same_row(c1, c2):
            c1_center = c1[1] + c1[3] - c1[3] / 2
            c2_bottom = c2[1] + c2[3]
            c2_top = c2[1]
            return c2_top < c1_center < c2_bottom

        orig_cells = [c for c in cells]
        rows = []
        while cells:
            first = cells[0]
            rest = cells[1:]
            cells_in_same_row = sorted(
                [
                    c for c in rest
                    if cell_in_same_row(c, first)
                ],
                key=lambda c: c[0]
            )

            row_cells = sorted([first] + cells_in_same_row, key=lambda c: c[0])
            rows.append(row_cells)
            cells = [
                c for c in rest
                if not cell_in_same_row(c, first)
            ]

        # Sort rows by average height of their center.
        def avg_height_of_center(row):
            centers = [y + h - h / 2 for x, y, w, h in row]
            return sum(centers) / len(centers)

        rows.sort(key=avg_height_of_center)
        cell_images_rows = []
        for row in rows:
            cell_images_row = []
            for x, y, w, h in row:
                cell_images_row.append(image[y:y+h, x:x+w])
            cell_images_rows.append(cell_images_row)
        return cell_images_rows

##### 5.2.5.2 table_ocr/extract_cells/__main__.py

Takes as a command line argument a path to an image of a table.

Detects cells in the table and extracts each cell to an image file in a new `/cells/` subdirectory in the same directory of the given image’s path.

Each cell filename is suffixed with `<row>-<column>` so that the filenames can be sorted lexicographically and will align with reading the cells from left-to-right, top-to-bottom.

Prints to stdout the lexicographically sorted list of filenames of the extracted cells.

    import os
    import sys

    import cv2

    from table_ocr.extract_cells import extract_cell_images_from_table

    def main(f):
        results = []
        directory, filename = os.path.split(f)
        table = cv2.imread(f, cv2.IMREAD_GRAYSCALE)
        rows = extract_cell_images_from_table(table)
        cell_img_dir = os.path.join(directory, "cells")
        os.makedirs(cell_img_dir, exist_ok=True)
        for i, row in enumerate(rows):
            for j, cell in enumerate(row):
                cell_filename = "{:03d}-{:03d}.png".format(i, j)
                path = os.path.join(cell_img_dir, cell_filename)
                cv2.imwrite(path, cell)
                print(path)

    def extract_cell_images_from_table(image):
        BLUR_KERNEL_SIZE = (17, 17)
        STD_DEV_X_DIRECTION = 0
        STD_DEV_Y_DIRECTION = 0
        blurred = cv2.GaussianBlur(image, BLUR_KERNEL_SIZE, STD_DEV_X_DIRECTION, STD_DEV_Y_DIRECTION)
        MAX_COLOR_VAL = 255
        BLOCK_SIZE = 15
        SUBTRACT_FROM_MEAN = -2

        img_bin = cv2.adaptiveThreshold(
            ~blurred,
            MAX_COLOR_VAL,
            cv2.ADAPTIVE_THRESH_MEAN_C,
            cv2.THRESH_BINARY,
            BLOCK_SIZE,
            SUBTRACT_FROM_MEAN,
        )
        vertical = horizontal = img_bin.copy()
        SCALE = 5
        image_width, image_height = horizontal.shape
        horizontal_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (int(image_width / SCALE), 1))
        horizontally_opened = cv2.morphologyEx(img_bin, cv2.MORPH_OPEN, horizontal_kernel)
        vertical_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (1, int(image_height / SCALE)))
        vertically_opened = cv2.morphologyEx(img_bin, cv2.MORPH_OPEN, vertical_kernel)

        horizontally_dilated = cv2.dilate(horizontally_opened, cv2.getStructuringElement(cv2.MORPH_RECT, (40, 1)))
        vertically_dilated = cv2.dilate(vertically_opened, cv2.getStructuringElement(cv2.MORPH_RECT, (1, 60)))

        mask = horizontally_dilated + vertically_dilated
        contours, heirarchy = cv2.findContours(
            mask, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE,
        )

        perimeter_lengths = [cv2.arcLength(c, True) for c in contours]
        epsilons = [0.05 * p for p in perimeter_lengths]
        approx_polys = [cv2.approxPolyDP(c, e, True) for c, e in zip(contours, epsilons)]

        # Filter out contours that aren't rectangular. Those that aren't rectangular
        # are probably noise.
        approx_rects = [p for p in approx_polys if len(p) == 4]
        bounding_rects = [cv2.boundingRect(a) for a in approx_polys]

        # Filter out rectangles that are too narrow or too short.
        MIN_RECT_WIDTH = 40
        MIN_RECT_HEIGHT = 10
        bounding_rects = [
            r for r in bounding_rects if MIN_RECT_WIDTH < r[2] and MIN_RECT_HEIGHT < r[3]
        ]

        # The largest bounding rectangle is assumed to be the entire table.
        # Remove it from the list. We don't want to accidentally try to OCR
        # the entire table.
        largest_rect = max(bounding_rects, key=lambda r: r[2] * r[3])
        bounding_rects = [b for b in bounding_rects if b is not largest_rect]

        cells = [c for c in bounding_rects]
        def cell_in_same_row(c1, c2):
            c1_center = c1[1] + c1[3] - c1[3] / 2
            c2_bottom = c2[1] + c2[3]
            c2_top = c2[1]
            return c2_top < c1_center < c2_bottom

        orig_cells = [c for c in cells]
        rows = []
        while cells:
            first = cells[0]
            rest = cells[1:]
            cells_in_same_row = sorted(
                [
                    c for c in rest
                    if cell_in_same_row(c, first)
                ],
                key=lambda c: c[0]
            )

            row_cells = sorted([first] + cells_in_same_row, key=lambda c: c[0])
            rows.append(row_cells)
            cells = [
                c for c in rest
                if not cell_in_same_row(c, first)
            ]

        # Sort rows by average height of their center.
        def avg_height_of_center(row):
            centers = [y + h - h / 2 for x, y, w, h in row]
            return sum(centers) / len(centers)

        rows.sort(key=avg_height_of_center)
        cell_images_rows = []
        for row in rows:
            cell_images_row = []
            for x, y, w, h in row:
                cell_images_row.append(image[y:y+h, x:x+w])
            cell_images_rows.append(cell_images_row)
        return cell_images_rows

    if __name__ == "__main__":
        main(sys.argv[1])

#### 5.2.6 table_ocr/ocr_image/

##### 5.2.6.1 table_ocr/ocr_image/__init__.py

    import math

    import cv2
    import numpy as np
    import pytesseract

    def crop_to_text(image):
        MAX_COLOR_VAL = 255
        BLOCK_SIZE = 15
        SUBTRACT_FROM_MEAN = -2

        img_bin = cv2.adaptiveThreshold(
            ~image,
            MAX_COLOR_VAL,
            cv2.ADAPTIVE_THRESH_MEAN_C,
            cv2.THRESH_BINARY,
            BLOCK_SIZE,
            SUBTRACT_FROM_MEAN,
        )

        img_h, img_w = image.shape
        horizontal_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (int(img_w * 0.5), 1))
        vertical_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (1, int(img_h * 0.7)))
        horizontal_lines = cv2.morphologyEx(img_bin, cv2.MORPH_OPEN, horizontal_kernel)
        vertical_lines = cv2.morphologyEx(img_bin, cv2.MORPH_OPEN, vertical_kernel)
        both = horizontal_lines + vertical_lines
        cleaned = img_bin - both

        # Get rid of little noise.
        kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (3, 3))
        opened = cv2.morphologyEx(cleaned, cv2.MORPH_OPEN, kernel)
        opened = cv2.dilate(opened, kernel)

        contours, hierarchy = cv2.findContours(opened, cv2.RETR_LIST, cv2.CHAIN_APPROX_SIMPLE)
        bounding_rects = [cv2.boundingRect(c) for c in contours]
        NUM_PX_COMMA = 6
        MIN_CHAR_AREA = 5 * 9
        char_sized_bounding_rects = [(x, y, w, h) for x, y, w, h in bounding_rects if w * h > MIN_CHAR_AREA]
        if char_sized_bounding_rects:
            minx, miny, maxx, maxy = math.inf, math.inf, 0, 0
            for x, y, w, h in char_sized_bounding_rects:
                minx = min(minx, x)
                miny = min(miny, y)
                maxx = max(maxx, x + w)
                maxy = max(maxy, y + h)
            x, y, w, h = minx, miny, maxx - minx, maxy - miny
            cropped = image[y:min(img_h, y+h+NUM_PX_COMMA), x:min(img_w, x+w)]
        else:
            # If we morphed out all of the text, assume an empty image.
            cropped = MAX_COLOR_VAL * np.ones(shape=(20, 100), dtype=np.uint8)
        bordered = cv2.copyMakeBorder(cropped, 5, 5, 5, 5, cv2.BORDER_CONSTANT, None, 255)
        return bordered
    def ocr_image(image, config):
        return pytesseract.image_to_string(
            image,
            config=config
        )

##### 5.2.6.2 table_ocr/ocr_image/__main__.py

This does a little bit of cleanup before sending it through tesseract.

Creates images and text files that can be used for training tesseract. See https://github.com/tesseract-ocr/tesstrain.

    import argparse
    import math
    import os
    import sys

    import cv2

    from table_ocr.ocr_image import crop_to_text, ocr_image

    description="""Takes a single argument that is the image to OCR.
    Remaining arguments are passed directly to Tesseract.

    Attempts to make OCR more accurate by performing some modifications on the image.
    Saves the modified image and the OCR text in an `ocr_data` directory.
    Filenames are of the format for training with tesstrain."""
    parser = argparse.ArgumentParser(description=description)
    parser.add_argument("image", help="filepath of image to perform OCR")

    def main(image_file, tess_args):
        directory, filename = os.path.split(image_file)
        filename_sans_ext, ext = os.path.splitext(filename)
        image = cv2.imread(image_file, cv2.IMREAD_GRAYSCALE)
        cropped = crop_to_text(image)
        ocr_data_dir = os.path.join(directory, "ocr_data")
        os.makedirs(ocr_data_dir, exist_ok=True)
        out_imagepath = os.path.join(ocr_data_dir, filename)
        out_txtpath = os.path.join(ocr_data_dir, "{}.gt.txt".format(filename_sans_ext))
        cv2.imwrite(out_imagepath, cropped)
        txt = ocr_image(cropped, " ".join(tess_args))
        print(txt)
        with open(out_txtpath, "w") as txt_file:
            txt_file.write(txt)

    if __name__ == "__main__":
        args, tess_args = parser.parse_known_args()
        main(args.image, tess_args)

#### 5.2.7 table_ocr/ocr_to_csv/

##### 5.2.7.1 table_ocr/ocr_to_csv/__init__.py

    import csv
    import io
    import os

    def text_files_to_csv(files):
        """Files must be sorted lexicographically
        Filenames must be <row>-<colum>.txt.
        000-000.txt
        000-001.txt
        001-000.txt
        etc...
        """
        rows = []
        for f in files:
            directory, filename = os.path.split(f)
            with open(f) as of:
                txt = of.read()
            row, column = map(int, filename.split(".")[0].split("-"))
            if row == len(rows):
                rows.append([])
            rows[row].append(txt)

        csv_file = io.StringIO()
        writer = csv.writer(csv_file)
        writer.writerows(rows)
        return csv_file.getvalue()

##### 5.2.7.2 table_ocr/ocr_to_csv/__main__.py

    import argparse
    import os

    from table_ocr.ocr_to_csv import text_files_to_csv

    parser = argparse.ArgumentParser()
    parser.add_argument("files", nargs="+")

    def main(files):
        print(text_files_to_csv(files))

    if __name__ == "__main__":
        args = parser.parse_args()
        files = args.files
        files.sort()
        main(files)

## 6 Utils

The following code lets us specify a size for images when they are exported to html.

Org supports specifying an export size for an image by putting the `#+ATTR_HTML: :width 100px` before the image. But since our images are in a results drawer, we need a way for our results drawer to do that for us automatically.

Adding `#+ATTR_HTML` after the beginning of the result block introduces a new problem. Org-babel no longer recognizes the result as a result block and doesn’t remove it when a src block is re-evaluated, so we end up just appending new results on each evaluation.

There is nothing configurable that will tell org-babel to remove our line. But we can define a function to do some cleanup and then add it as a before hook with `advice-add`.

    (concat "#+ATTR_HTML: :width " width " :height " height "\n[[file:" text "]]")

    (defun remove-attributes-from-src-block-result (&rest args)
      (let ((location (org-babel-where-is-src-block-result))
            (attr-regexp "[   ]*#\\+ATTR.*$"))
        (when location
          (save-excursion
            (goto-char location)
            (when (looking-at (concat org-babel-result-regexp ".*$"))
              (next-line)
              (while (looking-at attr-regexp)
                (kill-whole-line)))))))

    (advice-add 'org-babel-remove-result :before #'remove-attributes-from-src-block-result)
    (advice-add 'org-babel-execute-src-block :before #'remove-attributes-from-src-block-result)

### 6.1 Logging

    def get_logger(name):
        logger = logging.getLogger(name)
        lvl = os.environ.get("PY_LOG_LVL", "info").upper()
        handler = logging.StreamHandler()
        formatter = logging.Formatter(logging.BASIC_FORMAT)
        handler.setFormatter(formatter)
        logger.addHandler(handler)
        handler.setLevel(lvl)
        logger.setLevel(lvl)
        return logger

Author: Eric Ihli

Created: 2020-04-25 Sat 12:20