Merge pull request #54 from gsergeant/mosaic_reader

Reader for Mosaic files

biotracks/readfile.py

@@ -44,6 +44,7 @@ class AbstractReader(metaclass=ABCMeta):
     """\
     Common interface for all tracking data readers.
     """
+
     def __init__(self, fname, conf=None, log_level=None):
         """\
         Set the input file name for the reader.
@@ -302,11 +303,11 @@ def read_objects(self):
         cp_df.reset_index(inplace=True)
         for index, row in cp_df.iterrows():
             objects_dict[index] = [row[self.frame], row[self.x], row[self.y]]
-            objects_df = pd.DataFrame(
-                [[key, value[0], value[1], value[2]]
-                 for key, value in objects_dict.items()],
-                columns=[self.obj_id, self.frame, self.x, self.y]
-            )
+        objects_df = pd.DataFrame(
+            [[key, value[0], value[1], value[2]]
+             for key, value in objects_dict.items()],
+            columns=[self.obj_id, self.frame, self.x, self.y]
+        )
         objects_df.columns = [
             cmso.OBJECT_ID, cmso.FRAME_ID, cmso.X_COORD, cmso.Y_COORD
         ]
@@ -393,10 +394,27 @@ def read(self):
         self._links[cmso.LINK_ID] -= 1  # CELLMIA index is 1-based
 
 
+class MosaicReader(AbstractReader):
+
+    MOSAIC_COLS = ["Trajectory", "Frame", "x", "y", "z"]
+
+    def read(self):
+        mo_df = pd.read_csv(self.fname, sep=None, usecols=self.MOSAIC_COLS)
+        mo_df.reset_index(inplace=True)
+        cols = [cmso.OBJECT_ID, cmso.LINK_ID, cmso.FRAME_ID,
+                cmso.X_COORD, cmso.Y_COORD, cmso.Z_COORD]
+        mo_df.columns = cols
+        self._objects = mo_df.drop(cmso.LINK_ID, 1)
+        self._links = mo_df.drop(
+            [cmso.FRAME_ID, cmso.X_COORD, cmso.Y_COORD, cmso.Z_COORD], 1)
+        self._links[cmso.LINK_ID] -= 1
+
+
 class TracksReader(object):
     """\
     Generic reader that delegates to specific ones based on file extension.
     """
+
     def __init__(self, fname, conf=None, log_level=None):
         """\
         Initialize and store a specific reader based on filename extension.
@@ -411,14 +429,24 @@ def __init__(self, fname, conf=None, log_level=None):
             self.reader = TrackMateReader(
                 fname, conf=conf, log_level=log_level
             )
-        elif ext == '.csv':
-            self.reader = CellProfilerReader(
-                fname, conf=conf, log_level=log_level
-            )
-        elif ext == '.txt':
-            self.reader = CellmiaReader(
-                fname, conf=conf, log_level=log_level
-            )
+        elif ext in ['.csv', '.tsv', '.txt']:
+            # read header and delegate to correct reader
+            # this pandas method can read csv, tsv and txt files
+            df = pd.read_csv(fname, header=None, sep=None, nrows=1)
+            trackname = df.iloc[0, 0]
+            if trackname == 'ImageNumber':
+                self.reader = CellProfilerReader(
+                    fname, conf=conf, log_level=log_level
+                )
+            elif trackname == 'ID of track':
+                self.reader = CellmiaReader(
+                    fname, conf=conf, log_level=log_level
+                )
+            elif trackname == 'Trajectory':
+                self.reader = MosaicReader(
+                    fname, conf=conf, log_level=log_level
+                )
+
         elif ext == '.json':
             self.reader = BiotracksReader(
                 fname, conf=conf, log_level=log_level

examples/Mosaic/Readme.md

@@ -0,0 +1,41 @@
+## Mosaic example
+
+The example in the *Mosaic* directory was generated using the [MosaicSuite plugin](http://mosaic.mpi-cbg.de/?q=downloads/imageJ) for ImageJ/Fiji.
+
+Version used: `MosaicSuite-1.0.8`.
+
+### Example 1
+The dataset used in this example is the same used in the [TrackMate](../TrackMate) and other examples. The images were both detected and tracked using the Mosaic Particle Tracker tool.
+
+#### The test dataset
+The test dataset used can be uploaded in ImageJ:
+
+`File  ▶ Open Samples  ▶ Tracks for TrackMate (807K)`
+
+You can then open and run the Mosaic plugin selecting:
+
+`Plugins  ▶ Mosaic  ▶ Particle Tracker 2D/3D `
+
+Alternatively, you can download the data from this [link](http://fiji.sc/samples/FakeTracks.tif).
+
+#### Settings to reproduce the two examples
+To reproduce the example in this directory, you need to choose the following settings
+
+- Detection settings:
+    - Kernel radius: 5
+    - Cutoff radius: 0.01
+    - Percentile: 0.4
+- Tracking settings:
+    - Displacement: 10.0
+    - Linkrange: 3
+
+Once you run the tracking, you can select **All Trajectories to Table**, which opens an ImageJ table that you can save to disk.
+
+
+#### Running the data_package library
+Move to the example directory and run the data package creation script:
+
+```
+cd examples/Mosaic/example_1
+python ../../../scripts/create_dpkg.py mosaic_tracks.csv
+```

examples/Mosaic/example_1/biotracks.ini

@@ -0,0 +1,8 @@
+[TOP_LEVEL_INFO]
+author = paola masuzzo
+title = A CMSO data package representation of cell tracking data
+name = cmso_tracks
+author_institute = VIB
+author_email = [email protected]
+
+[TRACKING_DATA]

examples/Mosaic/example_1/dp/dp.json

@@ -0,0 +1,88 @@
+{
+    "author": "paola masuzzo",
+    "author_email": "[email protected]",
+    "author_institute": "VIB",
+    "name": "cmso_tracks",
+    "resources": [
+        {
+            "name": "cmso_objects_table",
+            "path": "objects.csv",
+            "schema": {
+                "fields": [
+                    {
+                        "constraints": {
+                            "unique": true
+                        },
+                        "description": "",
+                        "format": "default",
+                        "name": "cmso_object_id",
+                        "title": "",
+                        "type": "integer"
+                    },
+                    {
+                        "description": "",
+                        "format": "default",
+                        "name": "cmso_frame_id",
+                        "title": "",
+                        "type": "integer"
+                    },
+                    {
+                        "description": "",
+                        "format": "default",
+                        "name": "cmso_x_coord",
+                        "title": "",
+                        "type": "number"
+                    },
+                    {
+                        "description": "",
+                        "format": "default",
+                        "name": "cmso_y_coord",
+                        "title": "",
+                        "type": "number"
+                    },
+                    {
+                        "description": "",
+                        "format": "default",
+                        "name": "cmso_z_coord",
+                        "title": "",
+                        "type": "integer"
+                    }
+                ],
+                "primaryKey": "cmso_object_id"
+            }
+        },
+        {
+            "name": "cmso_links_table",
+            "path": "links.csv",
+            "schema": {
+                "fields": [
+                    {
+                        "description": "",
+                        "format": "default",
+                        "name": "cmso_object_id",
+                        "title": "",
+                        "type": "integer"
+                    },
+                    {
+                        "description": "",
+                        "format": "default",
+                        "name": "cmso_link_id",
+                        "title": "",
+                        "type": "integer"
+                    }
+                ],
+                "foreignKeys": [
+                    {
+                        "fields": "cmso_object_id",
+                        "reference": {
+                            "datapackage": "",
+                            "fields": "cmso_object_id",
+                            "resource": "cmso_objects_table"
+                        }
+                    }
+                ]
+            }
+        }
+    ],
+    "title": "A CMSO data package representation of cell tracking data"
+}