[feat] generalize methods to list

Author: bgallois

README.md

@@ -7,8 +7,39 @@
  ## Installation
  To install the module:
  ```
+ git clone https://github.com/FastTrackOrg/FastAnalysis.git
+ cd FastAnalysis
  pip install fastanalysis
  ```
 
  ## Development
- The project is under active development and do not have public API documentation, a more or less complete API documentation can be generated using Sphinx.
+ The project is under active development and do not have public API documentation, a more or less complete API documentation can be generated using Sphinx.
+ 
+ ## Documentation
+ 
+ ### Retrieve data from a tracking.txt file
+ A tracking.txt file can be loaded and several method are available to select objects and frames:
+ ```
+ import fastanalysis as fa
+ 
+ tracking = fa.Load("tracking.txt")
+ fa.isObjectsInFrame(0, 100) # Check if object with id 0 is in the 100th frame
+ fa.isObjectsInFrame([0, 1], 100) # Check if object with id 0 and 1 is in the 100th frame
+ a = tracking.getObjectsInFrames(0, 100) # Select data of the object with id 0 in the 100th frame
+ b = tracking.getObjectsInFrames([0,1], [100,101]) # Select data of the object with id 0 and 1 in the 100th and 101th frames
+ c = tracking.getObjects(0) # Select data of the object with id 0 for all the frames
+ d = tracking.getObjects([0,1]) # Select data of the object with id 0 and 1 for all the frames
+ e = tracking.getFrame(100) # Select data for all the objects in the 100th frame
+ f = tracking.getFrame([100,101]) # Select data for all the objects in the 100th and 101th frames
+ ```       
+ 
+ ### Export data
+ ```
+ 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.
+ ```
+ Two format are supported: csv and excel.

fastanalysis/load.py

@@ -38,53 +38,103 @@ def getObjectNumber(self):
         maxObj = len(set(self.tracking.id.values))
         return maxObj
 
-    def getObject(self, iD):
-        """Get the data for the object with id.
+    def getObjects(self, ids):
+        """Get the data for the objects with ids.
 
-        :param iD: Id of the object.
-        :type index: int
-        :return: Data for the object id.
+        :param iD: Id or list of ids of objects.
+        :type index: list | int
+        :return: Data for the objects with ids.
         :rtype: DataFrame
         """
-        objectData = self.tracking[self.tracking.id == iD]
+        if isinstance(ids, list):
+            objectData = self.tracking[self.tracking.id.isin(ids)]
+        else:
+            objectData = self.tracking[self.tracking.id == ids]
         return objectData
 
-    def getFrame(self, index):
-        """Get the data for the image number index.
+    def getFrames(self, indexes):
+        """Get the data for the images with number indexes.
 
         :param index: Index of the image.
-        :type index: int
-        :return: Data for the image index.
+        :type index: list | int
+        :return: Data for the images with indexes.
         :rtype: DataFrame
         """
-        objectData = self.tracking[self.tracking.imageNumber == index]
+        if isinstance(indexes, list):
+            objectData = self.tracking[self.tracking.imageNumber.isin(indexes)]
+        else:
+            objectData = self.tracking[self.tracking.imageNumber == indexes]
         return objectData
 
-    def getObjectInFrame(self, iD, index):
-        """Get the data for an object id is in a frame index.
+    def getObjectsInFrames(self, ids, indexes):
+        """Get the data for objects ids in frames indexes.
 
-        :param iD: [Id of the object.]
-        :type iD: int
-        :param index: Index of the image.
-        :type index: int
-        :return: True if object id in frame index.
-        :rtype: bool
+        :param ids: Ids of objects.
+        :type ids: list | int
+        :param index: Indexex of images.
+        :type index: list | int
+        :return: Data for objects ids in frames indexes.
+        :rtype: Dataframe
         """
-        data = self.tracking[(self.tracking.imageNumber == index)&(self.tracking.id == iD)]
+        if not isinstance(indexes, list):
+            indexes = [indexes]
+        if not isinstance(ids, list):
+            ids = [ids]
+        data = self.tracking[(self.tracking.imageNumber.isin(indexes))&(self.tracking.id.isin(ids))]
         return data
 
-    def isObjectInFrame(self, iD, index):
+    def isObjectsInFrame(self, ids, index):
         """Check if an object id is in a frame index.
 
-        :param iD: Id of the object.
-        :type index: int
+        :param ids: Ids of objects.
+        :type ids: list | int
         :param index: Index of the image.
         :type index: int
         :return: True if object id in frame index.
         :rtype: bool
         """
-        data = self.tracking[(self.tracking.imageNumber == index)&(self.tracking.id == iD)]
-        if data.empty:
-            return False
+        isIn = []
+        if isinstance(ids, list):
+            for iD in ids:
+                data = self.tracking[(self.tracking.imageNumber == index)&(self.tracking.id == iD)]
+                if data.empty:
+                    isIn.append(False)
+                else:
+                    isIn.append(True)
+            return isIn
         else:
-            return True
+            data = self.tracking[(self.tracking.imageNumber == index)&(self.tracking.id == ids)]
+            if data.empty:
+                return False
+            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.
+
+        :param path: Path to the saved file.
+        :type path: str
+        :param keys: List of features.
+        :type keys: list
+        :param ids: List of ids of object.
+        :type ids: list
+        :param indexes: List of indexes of images.
+        :type indexes: list
+        """
+        tracking = self.tracking
+        if indexes:
+            tracking = tracking[tracking.imageNumber.isin(indexes)]
+
+        if ids:
+            tracking = tracking[tracking.id.isin(ids)]
+
+        if keys:
+            tracking = tracking[keys]
+
+        if fmt == "csv":
+            tracking.to_csv(path, sep=delimiter, index=False)
+        elif fmt == "excel":
+            tracking.to_excel(path, index=False)
+
+
+

fastanalysis/tests/test_load.py

@@ -20,35 +20,88 @@ def test_object_number():
     objectNumber = load.Load("tests/tracking.txt").getObjectNumber()
     assert objectNumber == 207
 
-def test_get_object():
+def test_get_objects():
     """Test get the data for an object"""
     reference = pandas.read_csv("tests/tracking.txt", sep='\t')
-    tracking = load.Load("tests/tracking.txt").getObject(0)
+    tracking = load.Load("tests/tracking.txt").getObjects(0)
     pandas.testing.assert_frame_equal(tracking, reference[reference.id==0])
-    tracking = load.Load("tests/tracking.txt").getObject(1)
-    pandas.testing.assert_frame_equal(tracking, reference[reference.id==1])
+    tracking = load.Load("tests/tracking.txt").getObjects([0, 1])
+    pandas.testing.assert_frame_equal(tracking, reference[(reference.id==1)|(reference.id==0)])
 
-def test_get_frame():
+def test_get_frames():
     """Test get the data for a frame"""
     reference = pandas.read_csv("tests/tracking.txt", sep='\t')
-    tracking = load.Load("tests/tracking.txt").getFrame(10)
+    tracking = load.Load("tests/tracking.txt").getFrames(10)
     pandas.testing.assert_frame_equal(tracking, reference[reference.imageNumber==10])
-    tracking = load.Load("tests/tracking.txt").getFrame(1)
-    pandas.testing.assert_frame_equal(tracking, reference[reference.imageNumber==1])
+    tracking = load.Load("tests/tracking.txt").getFrames([1, 10])
+    pandas.testing.assert_frame_equal(tracking, reference[(reference.imageNumber==1)|(reference.imageNumber==10)])
 
-def test_get_object_in_frame():
+def test_get_objects_in_frames():
     """Test get the data for an frame"""
     reference = pandas.read_csv("tests/tracking.txt", sep='\t')
-    tracking = load.Load("tests/tracking.txt").getObjectInFrame(0, 200)
+    tracking = load.Load("tests/tracking.txt").getObjectsInFrames(0, 200)
     pandas.testing.assert_frame_equal(tracking, reference[(reference.imageNumber==200)&(reference.id==0)])
-    tracking = load.Load("tests/tracking.txt").getObjectInFrame(1, 100)
-    pandas.testing.assert_frame_equal(tracking, reference[(reference.imageNumber==100)&(reference.id==1)])
+    tracking = load.Load("tests/tracking.txt").getObjectsInFrames([1, 2], [0, 100])
+    pandas.testing.assert_frame_equal(tracking, reference[((reference.imageNumber==100)|(reference.imageNumber==0))&((reference.id==1)|(reference.id==2))])
 
-def test_is_object_in_frame():
-    """Test get the data for an frame"""
+def test_is_objects_in_frame():
+    """Test check if objects in frame"""
     reference = pandas.read_csv("tests/tracking.txt", sep='\t')
-    tracking = load.Load("tests/tracking.txt").isObjectInFrame(0, 0)
+    tracking = load.Load("tests/tracking.txt").isObjectsInFrame(0, 0)
     assert tracking
-    tracking = load.Load("tests/tracking.txt").isObjectInFrame(0, 1500)
+    tracking = load.Load("tests/tracking.txt").isObjectsInFrame(0, 1500)
     assert not tracking
 
+def test_export_csv():
+    """Test set the data in a file"""
+    reference = pandas.read_csv("tests/tracking.txt", sep='\t')
+    tracking = load.Load("tests/tracking.txt")
+
+    tracking.saved("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=',')
+    test = pandas.read_csv("tests/test.csv", sep=',')
+    pandas.testing.assert_frame_equal(reference, test)
+    
+    tracking.saved("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])
+    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])
+    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])
+    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)
+
+def test_export_excel():
+    """Test set the data in an excel file"""
+    reference = pandas.read_csv("tests/tracking.txt", sep='\t')
+    tracking = load.Load("tests/tracking.txt")
+
+    tracking.saved("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")
+    test = pandas.read_excel("tests/test.xlsx")
+    pandas.testing.assert_frame_equal(reference[["imageNumber"]], test)
+    
+    tracking.saved("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")
+    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")
+    test = pandas.read_excel("tests/test.xlsx")
+    pandas.testing.assert_frame_equal(reference[(reference.id==0) & (reference.imageNumber==0)].reset_index(drop=True), test)

requirements/conda.txt

@@ -1 +1,3 @@
 pandas
+xlrd
+openpyxl

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'],
+    install_requires=['pandas', 'numpy', 'matplotlib', 'xlrd', 'openpyxl'],
     license='MIT',
     python_requires='>=3.6',
     zip_safe=False