[MRG + 1] Create a new figure and test each plot type #127 (#179)

* [MRG] Create a new figure and test each plot type #127

 - move `plot()` to `plotting.py` as `plot_pdf()`
 - modify plotting functions to return matplotlib figures
 - add `test_plotting.py` and baseline images
 - import `plot_pdf()` in `__init__`
 - update `cli.py` to use `plot_pdf()`
 - update advanced usage docs to reflect changes

* Change matplotlib backend for image comparison tests

* Update plotting and tests
 - use matplotlib rectangle instead of `cv2.rectangle` in
`plot_contour()`
 - set matplotlib backend in `tests/__init__`
 - update contour plot baseline image
 - update `test_plotting` with more checks

* Update plot tests and config
 - remove unnecessary asserts
 - update setup.cfg and makefile with `--mpl`

* Add  to

* Add tolerance

* remove text from baseline plots
update plot tests with `remove_text`

* Change method name, update docs and add pep8

* Update docs

Makefile

@@ -15,7 +15,7 @@ install:
 	pip install ".[dev]"
 
 test:
-	pytest --verbose --cov-config .coveragerc --cov-report term --cov-report xml --cov=camelot tests
+	pytest --verbose --cov-config .coveragerc --cov-report term --cov-report xml --cov=camelot --mpl tests
 
 docs:
 	cd docs && make html
@@ -25,4 +25,4 @@ publish:
 	pip install twine
 	python setup.py sdist
 	twine upload dist/*
-	rm -fr build dist .egg camelot_py.egg-info
+	rm -fr build dist .egg camelot_py.egg-info

camelot/__init__.py

@@ -6,6 +6,7 @@ from click import HelpFormatter
 
 from .__version__ import __version__
 from .io import read_pdf
+from .plotting import plot
 
 
 def _write_usage(self, prog, args='', prefix='Usage: '):

camelot/cli.py

@@ -3,9 +3,11 @@
 import logging
 
 import click
+import matplotlib.pyplot as plt
 
 from . import __version__
 from .io import read_pdf
+from .plotting import plot
 
 
 logger = logging.getLogger('camelot')
@@ -81,7 +83,7 @@ def cli(ctx, *args, **kwargs):
               help='Number of times for erosion/dilation will be applied.')
 @click.option('-plot', '--plot_type',
               type=click.Choice(['text', 'table', 'contour', 'joint', 'line']),
-              help='Plot geometry found on PDF page, for debugging.')
+              help='Plot elements found on PDF page for visual debugging.')
 @click.argument('filepath', type=click.Path(exists=True))
 @pass_config
 def lattice(c, *args, **kwargs):
@@ -107,7 +109,8 @@ def lattice(c, *args, **kwargs):
     click.echo('Found {} tables'.format(tables.n))
     if plot_type is not None:
         for table in tables:
-            table.plot(plot_type)
+            plot(table, plot_type=plot_type)
+            plt.show()
     else:
         if output is None:
             raise click.UsageError('Please specify output file path using --output')
@@ -128,7 +131,7 @@ def lattice(c, *args, **kwargs):
               ' used to combine text horizontally, to generate columns.')
 @click.option('-plot', '--plot_type',
               type=click.Choice(['text', 'table']),
-              help='Plot geometry found on PDF page for debugging.')
+              help='Plot elements found on PDF page for visual debugging.')
 @click.argument('filepath', type=click.Path(exists=True))
 @pass_config
 def stream(c, *args, **kwargs):
@@ -153,7 +156,8 @@ def stream(c, *args, **kwargs):
     click.echo('Found {} tables'.format(tables.n))
     if plot_type is not None:
         for table in tables:
-            table.plot(plot_type)
+            plot(table, plot_type=plot_type)
+            plt.show()
     else:
         if output is None:
             raise click.UsageError('Please specify output file path using --output')

camelot/core.py

@@ -7,8 +7,6 @@ import tempfile
 import numpy as np
 import pandas as pd
 
-from .plotting import *
-
 
 class Cell(object):
     """Defines a cell in a table with coordinates relative to a
@@ -321,33 +319,6 @@ class Table(object):
                     cell.hspan = True
         return self
 
-    def plot(self, geometry_type):
-        """Plot geometry found on PDF page based on geometry_type
-        specified, useful for debugging and playing with different
-        parameters to get the best output.
-
-        Parameters
-        ----------
-        geometry_type : str
-            The geometry type for which a plot should be generated.
-            Can be 'text', 'table', 'contour', 'joint', 'line'
-
-        """
-        if self.flavor == 'stream' and geometry_type in ['contour', 'joint', 'line']:
-            raise NotImplementedError("{} cannot be plotted with flavor='stream'".format(
-                                       geometry_type))
-
-        if geometry_type == 'text':
-            plot_text(self._text)
-        elif geometry_type == 'table':
-            plot_table(self)
-        elif geometry_type == 'contour':
-            plot_contour(self._image)
-        elif geometry_type == 'joint':
-            plot_joint(self._image)
-        elif geometry_type == 'line':
-            plot_line(self._segments)
-
     def to_csv(self, path, **kwargs):
         """Writes Table to a comma-separated values (csv) file.
 

camelot/handlers.py

@@ -141,9 +141,6 @@ class PDFHandler(object):
         -------
         tables : camelot.core.TableList
             List of tables found in PDF.
-        geometry : camelot.core.GeometryList
-            List of geometry objects (contours, lines, joints) found
-            in PDF.
 
         """
         tables = []

camelot/plotting.py

@@ -1,15 +1,59 @@
-import cv2
+# -*- coding: utf-8 -*-
+
 import matplotlib.pyplot as plt
 import matplotlib.patches as patches
 
 
+def plot(table, plot_type='text', filepath=None):
+    """Plot elements found on PDF page based on plot_type
+    specified, useful for debugging and playing with different
+    parameters to get the best output.
+
+    Parameters
+    ----------
+    table: Table
+        A Camelot Table.
+    plot_type : str, optional (default: 'text')
+        {'text', 'table', 'contour', 'joint', 'line'}
+        The element type for which a plot should be generated.
+    filepath: str, optional (default: None)
+        Absolute path for saving the generated plot.
+
+    Returns
+    -------
+    fig : matplotlib.fig.Figure
+
+    """
+    if table.flavor == 'stream' and plot_type in ['contour', 'joint', 'line']:
+        raise NotImplementedError("{} cannot be plotted with flavor='stream'".format(
+                                    plot_type))
+    if plot_type == 'text':
+        fig = plot_text(table._text)
+    elif plot_type == 'table':
+        fig = plot_table(table)
+    elif plot_type == 'contour':
+        fig = plot_contour(table._image)
+    elif plot_type == 'joint':
+        fig = plot_joint(table._image)
+    elif plot_type == 'line':
+        fig = plot_line(table._segments)
+    if filepath:
+        plt.savefig(filepath)
+    return fig
+
+
 def plot_text(text):
-    """Generates a plot for all text present on the PDF page.
+    """Generates a plot for all text elements present
+    on the PDF page.
 
     Parameters
     ----------
     text : list
 
+    Returns
+    -------
+    fig : matplotlib.fig.Figure
+
     """
     fig = plt.figure()
     ax = fig.add_subplot(111, aspect='equal')
@@ -26,83 +70,116 @@ def plot_text(text):
         )
     ax.set_xlim(min(xs) - 10, max(xs) + 10)
     ax.set_ylim(min(ys) - 10, max(ys) + 10)
-    plt.show()
+    return fig
 
 
 def plot_table(table):
-    """Generates a plot for the table.
+    """Generates a plot for the detected tables
+    on the PDF page.
 
     Parameters
     ----------
     table : camelot.core.Table
 
+    Returns
+    -------
+    fig : matplotlib.fig.Figure
+
     """
+    fig = plt.figure()
+    ax = fig.add_subplot(111, aspect='equal')
     for row in table.cells:
         for cell in row:
             if cell.left:
-                plt.plot([cell.lb[0], cell.lt[0]],
+                ax.plot([cell.lb[0], cell.lt[0]],
                          [cell.lb[1], cell.lt[1]])
             if cell.right:
-                plt.plot([cell.rb[0], cell.rt[0]],
+                ax.plot([cell.rb[0], cell.rt[0]],
                          [cell.rb[1], cell.rt[1]])
             if cell.top:
-                plt.plot([cell.lt[0], cell.rt[0]],
+                ax.plot([cell.lt[0], cell.rt[0]],
                          [cell.lt[1], cell.rt[1]])
             if cell.bottom:
-                plt.plot([cell.lb[0], cell.rb[0]],
+                ax.plot([cell.lb[0], cell.rb[0]],
                          [cell.lb[1], cell.rb[1]])
-    plt.show()
+    return fig
 
 
 def plot_contour(image):
-    """Generates a plot for all table boundaries present on the
+    """Generates a plot for all table boundaries present
-    PDF page.
+    on the PDF page.
 
     Parameters
     ----------
     image : tuple
 
+    Returns
+    -------
+    fig : matplotlib.fig.Figure
+
     """
     img, table_bbox = image
+    fig = plt.figure()
+    ax = fig.add_subplot(111, aspect='equal')
     for t in table_bbox.keys():
-        cv2.rectangle(img, (t[0], t[1]),
+        ax.add_patch(
-                      (t[2], t[3]), (255, 0, 0), 20)
+            patches.Rectangle(
-    plt.imshow(img)
+                (t[0], t[1]),
-    plt.show()
+                t[2] - t[0],
+                t[3] - t[1],
+                fill=None,
+                edgecolor='red'
+            )
+        )
+    ax.imshow(img)
+    return fig
 
 
 def plot_joint(image):
-    """Generates a plot for all line intersections present on the
+    """Generates a plot for all line intersections present
-    PDF page.
+    on the PDF page.
 
     Parameters
     ----------
     image : tuple
 
+    Returns
+    -------
+    fig : matplotlib.fig.Figure
+
     """
     img, table_bbox = image
+    fig = plt.figure()
+    ax = fig.add_subplot(111, aspect='equal')
     x_coord = []
     y_coord = []
     for k in table_bbox.keys():
         for coord in table_bbox[k]:
             x_coord.append(coord[0])
             y_coord.append(coord[1])
-    plt.plot(x_coord, y_coord, 'ro')
+    ax.plot(x_coord, y_coord, 'ro')
-    plt.imshow(img)
+    ax.imshow(img)
-    plt.show()
+    return fig
 
 
 def plot_line(segments):
-    """Generates a plot for all line segments present on the PDF page.
+    """Generates a plot for all line segments present
+    on the PDF page.
 
     Parameters
     ----------
     segments : tuple
 
+    Returns
+    -------
+    fig : matplotlib.fig.Figure
+
     """
+    fig = plt.figure()
+    ax = fig.add_subplot(111, aspect='equal')
     vertical, horizontal = segments
     for v in vertical:
-        plt.plot([v[0], v[2]], [v[1], v[3]])
+        ax.plot([v[0], v[2]], [v[1], v[3]])
     for h in horizontal:
-        plt.plot([h[0], h[2]], [h[1], h[3]])
+        ax.plot([h[0], h[2]], [h[1], h[3]])
-    plt.show()
+    return fig

docs/user/advanced.rst

@@ -27,12 +27,12 @@ To process background lines, you can pass ``process_background=True``.
 .. csv-table::
   :file: ../_static/csv/background_lines.csv
 
-Plot geometry
+Visual debugging
--------------
+----------------
 
-You can use a :class:`table <camelot.core.Table>` object's :meth:`plot() <camelot.core.TableList.plot>` method to plot various geometries that were detected by Camelot while processing the PDF page. This can help you select table areas, column separators and debug bad table outputs, by tweaking different configuration parameters.
+You can use the :meth:`plot() <camelot.plotting.plot>` method to generate a `matplotlib <https://matplotlib.org/>`_ plot of various elements that were detected on the PDF page while processing it. This can help you select table areas, column separators and debug bad table outputs, by tweaking different configuration parameters.
 
-The following geometries are available for plotting. You can pass them to the :meth:`plot() <camelot.core.TableList.plot>` method, which will then generate a `matplotlib <https://matplotlib.org/>`_ plot for the passed geometry.
+You can specify the type of element you want to plot using the ``plot_type`` keyword argument. The generated plot can be saved to a file by passing a ``filename`` keyword argument. The following plot types are supported:
 
 - 'text'
 - 'table'
@@ -40,9 +40,9 @@ The following geometries are available for plotting. You can pass them to the :m
 - 'line'
 - 'joint'
 
-.. note:: The last three geometries can only be used with :ref:`Lattice <lattice>`, i.e. when ``flavor='lattice'``.
+.. note:: The last three plot types can only be used with :ref:`Lattice <lattice>`, i.e. when ``flavor='lattice'``.
 
-Let's generate a plot for each geometry using this `PDF <../_static/pdf/foo.pdf>`__ as an example. First, let's get all the tables out.
+Let's generate a plot for each type using this `PDF <../_static/pdf/foo.pdf>`__ as an example. First, let's get all the tables out.
 
 ::
 
@@ -59,7 +59,8 @@ Let's plot all the text present on the table's PDF page.
 
 ::
 
-    >>> tables[0].plot('text')
+    >>> camelot.plot(tables[0], plot_type='text')
+    >>> plt.show()
 
 .. figure:: ../_static/png/geometry_text.png
     :height: 674
@@ -77,11 +78,12 @@ This, as we shall later see, is very helpful with :ref:`Stream <stream>` for not
 table
 ^^^^^
 
-Let's plot the table (to see if it was detected correctly or not). This geometry type, along with contour, line and joint is useful for debugging and improving the extraction output, in case the table wasn't detected correctly. (More on that later.)
+Let's plot the table (to see if it was detected correctly or not). This plot type, along with contour, line and joint is useful for debugging and improving the extraction output, in case the table wasn't detected correctly. (More on that later.)
 
 ::
 
-    >>> tables[0].plot('table')
+    >>> camelot.plot(tables[0], plot_type='table')
+    >>> plt.show()
 
 .. figure:: ../_static/png/geometry_table.png
     :height: 674
@@ -101,7 +103,8 @@ Now, let's plot all table boundaries present on the table's PDF page.
 
 ::
 
-    >>> tables[0].plot('contour')
+    >>> camelot.plot(tables[0], plot_type='contour')
+    >>> plt.show()
 
 .. figure:: ../_static/png/geometry_contour.png
     :height: 674
@@ -119,7 +122,8 @@ Cool, let's plot all line segments present on the table's PDF page.
 
 ::
 
-    >>> tables[0].plot('line')
+    >>> camelot.plot(tables[0], plot_type='line')
+    >>> plt.show()
 
 .. figure:: ../_static/png/geometry_line.png
     :height: 674
@@ -137,7 +141,8 @@ Finally, let's plot all line intersections present on the table's PDF page.
 
 ::
 
-    >>> tables[0].plot('joint')
+    >>> camelot.plot(tables[0], plot_type='joint')
+    >>> plt.show()
 
 .. figure:: ../_static/png/geometry_joint.png
     :height: 674

setup.cfg

@@ -2,5 +2,5 @@
 test=pytest
 
 [tool:pytest]
-addopts = --verbose --cov-config .coveragerc --cov-report term --cov-report xml --cov=camelot tests
+addopts = --verbose --cov-config .coveragerc --cov-report term --cov-report xml --cov=camelot --mpl tests
-python_files = tests/test_*.py
+python_files = tests/test_*.py

setup.py

@@ -32,7 +32,8 @@ dev_requires = [
     'pytest>=3.8.0',
     'pytest-cov>=2.6.0',
     'pytest-runner>=4.2',
-    'Sphinx>=1.7.9'
+    'Sphinx>=1.7.9',
+    'pytest-mpl>=0.10'
 ]
 dev_requires = dev_requires + all_requires
 

tests/__init__.py

@@ -0,0 +1,2 @@
+import matplotlib
+matplotlib.use('agg')

tests/test_plotting.py

@@ -0,0 +1,51 @@
+# -*- coding: utf-8 -*-
+
+import os
+
+import pytest
+
+import camelot
+
+
+testdir = os.path.dirname(os.path.abspath(__file__))
+testdir = os.path.join(testdir, "files")
+
+
+@pytest.mark.mpl_image_compare(
+    baseline_dir="files/baseline_plots", remove_text=True)
+def test_text_plot():
+    filename = os.path.join(testdir, "foo.pdf")
+    tables = camelot.read_pdf(filename)
+    return camelot.plot(tables[0], plot_type='text')
+
+
+@pytest.mark.mpl_image_compare(
+    baseline_dir="files/baseline_plots", remove_text=True)
+def test_table_plot():
+    filename = os.path.join(testdir, "foo.pdf")
+    tables = camelot.read_pdf(filename)
+    return camelot.plot(tables[0], plot_type='table')
+
+
+@pytest.mark.mpl_image_compare(
+    baseline_dir="files/baseline_plots", remove_text=True)
+def test_contour_plot():
+    filename = os.path.join(testdir, "foo.pdf")
+    tables = camelot.read_pdf(filename)
+    return camelot.plot(tables[0], plot_type='contour')
+
+
+@pytest.mark.mpl_image_compare(
+    baseline_dir="files/baseline_plots", remove_text=True)
+def test_line_plot():
+    filename = os.path.join(testdir, "foo.pdf")
+    tables = camelot.read_pdf(filename)
+    return camelot.plot(tables[0], plot_type='line')
+
+
+@pytest.mark.mpl_image_compare(
+    baseline_dir="files/baseline_plots", remove_text=True)
+def test_joint_plot():
+    filename = os.path.join(testdir, "foo.pdf")
+    tables = camelot.read_pdf(filename)
+    return camelot.plot(tables[0], plot_type='joint')