[feat] update api

Author: bgallois

README.md

@@ -38,9 +38,9 @@
  import fastanalysis as fa
  
  tracking = fa.Load("tracking.txt")
- keys = fa.keys() # List saved features
- 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.
+ keys = fa.keys() # List export features
+ fa.export("output.xlsx", delimiter='\t', keys=["xHead", "yHead", "imageNumber", "id"], ids=None, indexes=None, format="excel") # Export a list of features for all the frames and all the objects in an excel file.
+ fa.export("output.txt", delimiter='\t', keys=None, ids=None, indexes=None, format="excel") # Export all thefeatures for all the frames and all the objects in an csv file.
  ```
  Two format are supported: csv and excel.
 
@@ -54,4 +54,4 @@
  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
- ```
+ ```

fastanalysis/load.py

@@ -5,7 +5,7 @@ class Load:
     """Base class to load tracking.txt files"""
 
     def __init__(self, path):
-        """Constructor for Load class.
+        """Constructor for the Load tracking object.
 
         :param path: Path to the tracking.txt file.
         :type path: str
@@ -18,7 +18,7 @@ def __init__(self, path):
             raise e
 
     def getDataframe(self):
-        """Get the tracking data in a DataFrame.
+        """Get the tracking data in a pandas DataFrame format.
 
         :raises Exception: The selected file is empty
         :return: Tracking data
@@ -30,7 +30,7 @@ def getDataframe(self):
             return self.tracking
 
     def getObjectNumber(self):
-        """Get the total number of objects.
+        """Get the total number of objects in the tracking file.
 
         :return: [Total number of objects]
         :rtype: [int]
@@ -39,7 +39,7 @@ def getObjectNumber(self):
         return maxObj
 
     def getObjects(self, ids):
-        """Get the data for the objects with ids.
+        """Get the tracking data for a list of objects.
 
         :param iD: Id or list of ids of objects.
         :type index: list | int
@@ -53,10 +53,10 @@ def getObjects(self, ids):
         return objectData
 
     def getFrames(self, indexes):
-        """Get the data for the images with number indexes.
+        """Get the tracking data for a list of images.
 
-        :param index: Index of the image.
-        :type index: list | int
+        :param indexes: Indexes of the images.
+        :type indexes: list | int
         :return: Data for the images with indexes.
         :rtype: DataFrame
         """
@@ -67,7 +67,7 @@ def getFrames(self, indexes):
         return objectData
 
     def getObjectsInFrames(self, ids, indexes):
-        """Get the data for objects ids in frames indexes.
+        """Get the tracking data for a list of objects in a list of frames.
 
         :param ids: Ids of objects.
         :type ids: list | int
@@ -84,7 +84,7 @@ def getObjectsInFrames(self, ids, indexes):
         return data
 
     def isObjectsInFrame(self, ids, index):
-        """Check if an object id is in a frame index.
+        """Check if a list of object is in a frame.
 
         :param ids: Ids of objects.
         :type ids: list | int
@@ -109,8 +109,8 @@ def isObjectsInFrame(self, ids, index):
             else:
                 return True
 
-    def saved(self, path, delimiter='\t', keys=None, ids=None, indexes=None, fmt="csv"):
-        """Check if an object id is in a frame index.
+    def export(self, path, delimiter='\t', keys=None, ids=None, indexes=None, fmt="csv"):
+        """Export the tracking data.
 
         :param path: Path to the saved file.
         :type path: str
@@ -135,6 +135,3 @@ def saved(self, path, delimiter='\t', keys=None, ids=None, indexes=None, fmt="cs
             tracking.to_csv(path, sep=delimiter, index=False)
         elif fmt == "excel":
             tracking.to_excel(path, index=False)
-
-
-

fastanalysis/tests/test_load.py

@@ -57,27 +57,27 @@ def test_export_csv():
     reference = pandas.read_csv("tests/tracking.txt", sep='\t')
     tracking = load.Load("tests/tracking.txt")
 
-    tracking.saved("tests/test.csv")
+    tracking.export("tests/test.csv")
     test = pandas.read_csv("tests/test.csv", sep='\t')
     pandas.testing.assert_frame_equal(reference, test)
 
-    tracking.saved("tests/test.csv", delimiter=',')
+    tracking.export("tests/test.csv", delimiter=',')
     test = pandas.read_csv("tests/test.csv", sep=',')
     pandas.testing.assert_frame_equal(reference, test)
 
-    tracking.saved("tests/test.csv", keys=["imageNumber"])
+    tracking.export("tests/test.csv", keys=["imageNumber"])
     test = pandas.read_csv("tests/test.csv", sep='\t')
     pandas.testing.assert_frame_equal(reference[["imageNumber"]], test)
 
-    tracking.saved("tests/test.csv", indexes=[1])
+    tracking.export("tests/test.csv", indexes=[1])
     test = pandas.read_csv("tests/test.csv", sep='\t')
     pandas.testing.assert_frame_equal(reference[reference.imageNumber==1].reset_index(drop=True), test)
 
-    tracking.saved("tests/test.csv", ids=[0])
+    tracking.export("tests/test.csv", ids=[0])
     test = pandas.read_csv("tests/test.csv", sep='\t')
     pandas.testing.assert_frame_equal(reference[reference.id==0].reset_index(drop=True), test)
 
-    tracking.saved("tests/test.csv", ids=[0], indexes=[0])
+    tracking.export("tests/test.csv", ids=[0], indexes=[0])
     test = pandas.read_csv("tests/test.csv", sep='\t')
     pandas.testing.assert_frame_equal(reference[(reference.id==0) & (reference.imageNumber==0)].reset_index(drop=True), test)
 
@@ -86,22 +86,22 @@ def test_export_excel():
     reference = pandas.read_csv("tests/tracking.txt", sep='\t')
     tracking = load.Load("tests/tracking.txt")
 
-    tracking.saved("tests/test.xlsx", fmt="excel")
+    tracking.export("tests/test.xlsx", fmt="excel")
     test = pandas.read_excel("tests/test.xlsx")
     pandas.testing.assert_frame_equal(reference, test)
 
-    tracking.saved("tests/test.xlsx", keys=["imageNumber"], fmt="excel")
+    tracking.export("tests/test.xlsx", keys=["imageNumber"], fmt="excel")
     test = pandas.read_excel("tests/test.xlsx")
     pandas.testing.assert_frame_equal(reference[["imageNumber"]], test)
 
-    tracking.saved("tests/test.xlsx", indexes=[1], fmt="excel")
+    tracking.export("tests/test.xlsx", indexes=[1], fmt="excel")
     test = pandas.read_excel("tests/test.xlsx")
     pandas.testing.assert_frame_equal(reference[reference.imageNumber==1].reset_index(drop=True), test)
 
-    tracking.saved("tests/test.xlsx", ids=[0], fmt="excel")
+    tracking.export("tests/test.xlsx", ids=[0], fmt="excel")
     test = pandas.read_excel("tests/test.xlsx")
     pandas.testing.assert_frame_equal(reference[reference.id==0].reset_index(drop=True), test)
 
-    tracking.saved("tests/test.xlsx", ids=[0], indexes=[0], fmt="excel")
+    tracking.export("tests/test.xlsx", ids=[0], indexes=[0], fmt="excel")
     test = pandas.read_excel("tests/test.xlsx")
     pandas.testing.assert_frame_equal(reference[(reference.id==0) & (reference.imageNumber==0)].reset_index(drop=True), test)