[feat] add Plot class

Author: bgallois

README.md

@@ -42,4 +42,16 @@
  fa.saved("output.xlsx", delimiter='\t', keys=["xHead", "yHead", "imageNumber", "id"], ids=None, indexes=None, format="excel") # Saved a list of features for all the frames and all the objects in an excel file.
  fa.saved("output.txt", delimiter='\t', keys=None, ids=None, indexes=None, format="excel") # Saved all thefeatures for all the frames and all the objects in an csv file.
  ```
- Two format are supported: csv and excel.
+ Two format are supported: csv and excel.
+ 
+ ### Plot metrics
+ ```
+ import fastanalysis as fa
+ import matplotlib.pyplot as plt
+ 
+ tracking = fa.Load("tracking.txt")
+ plotObj = fa.Plot(tracking)
+ plotObj.velocityDistribution(ids=[0, 1], key="Body", pooled=False, subplots=True) # Plot velocity distribution for objects 1 and 0 in 2 subplots
+ plotObj.velocityDistribution(ids=[0, 1], key="Body", pooled=False, subplots=False) # Plot velocity distribution for objects 1 and 0 in 1 plot
+ plotObj.velocityDistribution(ids=[0, 1], key="Body", pooled=True) # Plot velocity distribution for objects 1 and 0 pooled in 1 distribution
+ ```

docs/source/conf.py

@@ -44,7 +44,12 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = 'p-main_theme'
+import os
+from PSphinxTheme import utils
+
+p, html_theme, needs_sphinx = utils.set_psphinxtheme(html_theme)
+html_theme_path = p
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

docs/source/fastanalysis.rst

@@ -7,7 +7,12 @@ Submodules
 fastanalysis module
 -----------------------------
 
-.. automodule:: fastanalysis.load
+.. autoclass:: fastanalysis.load.Load
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. autoclass:: fastanalysis.plot.Plot
     :members:
     :undoc-members:
     :show-inheritance:

docs/source/index.rst

@@ -6,6 +6,18 @@
 Welcome to FastAnalysis's documentation!
 ========================================
 
+Introduction
+########################################
+FastAnalysis is a python module to load, export and analyse the output files of FastTrack software.
+
+Installation
+########################################
+.. code-block::
+
+   git clone https://github.com/FastTrackOrg/FastAnalysis.git
+   cd FastAnalysis
+   pip install -U .
+
 .. toctree::
    :maxdepth: 2
    :caption: Contents:

fastanalysis/__init__.py

@@ -1 +1,2 @@
 from .load import Load
+from .plot import Plot

fastanalysis/plot.py

@@ -0,0 +1,63 @@
+import pandas
+import numpy as np
+import matplotlib.pyplot as plt
+import seaborn as sns
+
+class Plot:
+    """Base class for plotting"""
+
+    def __init__(self, loadObject):
+        """Constructor for the plot object.
+
+        :param loadObject: A Load object containing the data.
+        :type index: Load
+        """
+        self.data = loadObject.getDataframe()
+
+    def velocityDistribution(self, ids, indexes=None, key="Body", pooled=True, subplots=False):
+        """Plot the velocity distribution.
+
+        :param ids: Ids of objects.
+        :type ids: list
+        :param indexes: Sub part of data based on indexes [min:max[ to select. Default: all the indexes.
+        :type ids: list
+        :param key: Head, Body or Tail. default: Body
+        :type key: str
+        :param pooled: Concatenate the objects distributions.
+        :type pooled: bool
+        :param subplots: Plot the distribution on separate subplots.
+        :type pooled: bool
+        :return: Matplotlib axe and raw data.
+        :rtype: (ax, list)
+        """
+        if not indexes:
+            indexes = (0, len(self.data.imageNumber.values))
+        if pooled:
+            subplots = False
+            tmpData = self.data[(self.data.id == ids[0])&(self.data.imageNumber.isin(range(indexes[0], indexes[1])))]
+            pooledData = (np.sqrt(np.diff(tmpData["x"+key].values)**2 + np.diff(tmpData["y"+key].values)**2)) / np.diff(tmpData.imageNumber.values)
+            for i in ids[1::]:
+                tmpData = self.data[(self.data.id == i)&(self.data.imageNumber.isin(range(indexes[0], indexes[1])))]
+                pooledData = np.concatenate((pooledData, (np.sqrt(np.diff(tmpData["x"+key].values)**2 + np.diff(tmpData["y"+key].values)**2)) / np.diff(tmpData.imageNumber.values)))
+            outputData = [pooledData]
+        else:
+            data = []
+            for i in ids:
+                tmpData = self.data[(self.data.id == i)&(self.data.imageNumber.isin(range(indexes[0], indexes[1])))]
+                data.append((np.sqrt(np.diff(tmpData["x"+key].values)**2 + np.diff(tmpData["y"+key].values)**2)) / np.diff(tmpData.imageNumber.values))
+            outputData = data
+
+        if subplots:
+            fig, axs = plt.subplots(len(ids), 1, sharey=True)
+            for i, j in enumerate(outputData):
+                sns.distplot(j, ax=axs[i], label=ids[i])
+                axs[i].legend()
+            axs[-1].set_xlabel("Velocity")
+        else:
+            fig, axs = plt.subplots()
+            for i, j in enumerate(outputData):
+                sns.distplot(j, ax=axs, label=ids[i])
+            axs.legend()
+            axs.set_xlabel("Velocity")
+
+        return (axs, outputData)

fastanalysis/tests/test_plot.py

@@ -0,0 +1,49 @@
+import pytest
+import pandas
+import numpy as np
+
+import load
+import plot
+
+
+def test_velocity_dist_default_key():
+    """Test velocity distribution."""
+    tracking = load.Load("tests/tracking.txt")
+    plotObj = plot.Plot(tracking)
+    velocityTest = plotObj.velocityDistribution(ids=[0, 1])
+    refData = tracking.getObjects(0)
+    a = (np.sqrt(np.diff(refData.xBody.values)**2 + np.diff(refData.yBody.values)**2)) / np.diff(refData.imageNumber.values)
+    refData = tracking.getObjects(1)
+    b = (np.sqrt(np.diff(refData.xBody.values)**2 + np.diff(refData.yBody.values)**2)) / np.diff(refData.imageNumber.values)
+    pooled = np.concatenate((a, b))
+    np.testing.assert_array_equal(pooled, velocityTest[1][0])
+
+    velocityTest = plotObj.velocityDistribution(ids=[0, 1], pooled=False)
+    np.testing.assert_array_equal(a, velocityTest[1][0])
+    np.testing.assert_array_equal(b, velocityTest[1][1])
+
+    refData = tracking.getObjectsInFrames(0, indexes=list(range(0, 100)))
+    a = (np.sqrt(np.diff(refData.xBody.values)**2 + np.diff(refData.yBody.values)**2)) / np.diff(refData.imageNumber.values)
+    velocityTest = plotObj.velocityDistribution(ids=[0], pooled=True, indexes=(0, 100))
+    np.testing.assert_array_equal(a, velocityTest[1][0])
+
+def test_velocity_dist_head():
+    """Test velocity distribution."""
+    tracking = load.Load("tests/tracking.txt")
+    plotObj = plot.Plot(tracking)
+    velocityTest = plotObj.velocityDistribution(ids=[0, 1], key="Head")
+    refData = tracking.getObjects(0)
+    a = (np.sqrt(np.diff(refData.xHead.values)**2 + np.diff(refData.yHead.values)**2)) / np.diff(refData.imageNumber.values)
+    refData = tracking.getObjects(1)
+    b = (np.sqrt(np.diff(refData.xHead.values)**2 + np.diff(refData.yHead.values)**2)) / np.diff(refData.imageNumber.values)
+    pooled = np.concatenate((a, b))
+    np.testing.assert_array_equal(pooled, velocityTest[1][0])
+
+    velocityTest = plotObj.velocityDistribution(ids=[0, 1], pooled=False, key="Head")
+    np.testing.assert_array_equal(a, velocityTest[1][0])
+    np.testing.assert_array_equal(b, velocityTest[1][1])
+
+    refData = tracking.getObjectsInFrames(0, indexes=list(range(0, 100)))
+    a = (np.sqrt(np.diff(refData.xHead.values)**2 + np.diff(refData.yHead.values)**2)) / np.diff(refData.imageNumber.values)
+    velocityTest = plotObj.velocityDistribution(ids=[0], pooled=True, indexes=(0, 100), key="Head")
+    np.testing.assert_array_equal(a, velocityTest[1][0])

requirements/conda.txt

@@ -1,3 +1,6 @@
 pandas
 xlrd
 openpyxl
+matplotlib
+seaborn
+numpy

setup.py

@@ -8,7 +8,7 @@
     description="A python library to open the tracking data from FastTrack the tracking software",
     url="https://github.com/FastTrackOrg/FastAnalysis",
     packages=['fastanalysis'],
-    install_requires=['pandas', 'numpy', 'matplotlib', 'xlrd', 'openpyxl'],
+    install_requires=['pandas', 'numpy', 'matplotlib', 'xlrd', 'openpyxl', 'seaborn'],
     license='MIT',
     python_requires='>=3.6',
     zip_safe=False