Adds new variable that outputs the gray value corresponding to the position of the fly in the grayscale mask #84

nazabic · 2017-11-07T16:00:38Z

No description provided.

…s values after the affine transformation

… in of the position of the fly on the mask.

…nd type, otherwise regions = mask and throw exceptions

qgeissmann · 2017-11-07T17:07:34Z

src/ethoscope/core/roi.py

        :param value: an optional value to be save for this ROI (e.g. to define left and right side)
        :param orientation: Optional orientation Not implemented yet
-        :param regions: Optional sub-regions within the ROI. Not implemented yet
+        :param regions: Optional sub-regions within the ROI.


We need to make it clear, in the doc, that regions is a 2d array and that regions is a greyscale map / LUT. I.e. each pixel is the value of region in X,Y

qgeissmann · 2017-11-07T17:07:55Z

src/ethoscope/core/roi.py

+        if gray_value is None:
+            return 0
+        else:
+            print gray_value, self.idx


remove print

qgeissmann · 2017-11-07T17:09:13Z

src/ethoscope/core/variables.py

        out += oy
        return YPosVariable(out)

+class RegionPosVariable(BaseIntVariable):


rename to RegionValueVariable: Pos suggest we are dealing with a position

qgeissmann · 2017-11-07T17:10:28Z

src/ethoscope/trackers/adaptive_bg_tracker.py

        phi_var = PhiVariable(int(round(angle)))
        # mlogl =   mLogLik(int(distance*1000))

+        gray_region = self._roi.find_region(x_var, y_var)


great idea, gray -> grey

qgeissmann · 2017-11-07T17:18:36Z

src/ethoscope/core/roi.py

+            self._regions = regions
+        else:
+            self._regions = self._mask
+            logging.warning('The regions argument of the roi has to be an numpy.ndarray that has equal size with the mask of the roi')


make error instead:

logging.error("xxxx") raise Exception("Regions and Mask hvae different sizes!")

qgeissmann · 2017-11-07T17:18:58Z

src/ethoscope/core/roi.py


+        if regions is None:
+            self._regions = self._mask
+        elif (regions.size == self._mask.size) & (type(regions) == type(self._mask)):


use ndarray.shape to do all in one go

qgeissmann · 2017-11-07T17:23:33Z

src/ethoscope/core/roi.py

+    def find_region(self, x, y):
+        try:
+            gray_value = self._regions[x, y]
+        except:


always print exception as a warning:

try: gray_value = self._regions[x, y] except Exception as e: logging.warning(e) ...

Also you can specify the type of exceptions Expect IndexError as e.

qgeissmann · 2017-11-07T17:24:40Z

src/ethoscope/core/variables.py

+    """
+    Type encoding a region inside the ROI, represented as the grayscale value of the pixel on which sits the center of the detected object.
+    """
+    header_name = "gray_region"


header_name = "sub_roi"

qgeissmann · 2017-11-07T17:25:15Z

src/ethoscope/core/variables.py

+    Type encoding a region inside the ROI, represented as the grayscale value of the pixel on which sits the center of the detected object.
+    """
+    header_name = "gray_region"
+    functional_type = "color"


functional_type = "grey_value" (UK spelling :D)

qgeissmann · 2017-11-07T17:25:53Z

src/ethoscope/drawers/drawers.py


 from ethoscope.utils.description import DescribedObject
 import os
+import numpy as np


remove if unneeded

qgeissmann · 2017-11-07T17:31:50Z

src/ethoscope/core/roi.py

-        return out, self._mask
+        return out, self._mask
+
+    def find_region(self, x, y):


rename to find_sub_region

qgeissmann · 2017-11-07T17:32:07Z

src/ethoscope/core/roi.py

        :param orientation: Optional orientation Not implemented yet
-        :param regions: Optional sub-regions within the ROI. Not implemented yet
+        :param regions: Optional sub-regions within the ROI.
+        :type regions: :class:`~numpy.ndarray`


rename to subregions

qgeissmann

almost there!!!

qgeissmann · 2017-11-10T17:57:16Z

src/ethoscope/core/roi.py

+        elif sub_rois.shape == self._mask.shape:
+            self._sub_rois = sub_rois
+        else:
+            self._sub_rois = self._mask


we can remove this line

qgeissmann · 2017-11-10T18:02:03Z

src/ethoscope/core/roi.py

+    def find_sub_roi(self, x, y):
+        try:
+            grey_value = self._sub_rois[x, y]
+        except Exception, e:


except Exception as e:

qgeissmann · 2017-11-10T18:08:27Z

src/ethoscope/core/variables.py

        out += oy
        return YPosVariable(out)

+class SubRoiValueVariable(BaseIntVariable):


Make a new base class: BaseTinyIntVariable, and derive SubRoiValueVariable from it.
Also, verify that you can store a unsigned (8b)int inside. "TINYINT UNSIGNED" ? check that SQLite supports it (not only MySQL).

…y subrois.

…abase, and a few name refactorings.

qgeissmann · 2017-11-14T17:20:46Z

src/ethoscope/core/variables.py

        _, oy = roi.offset
        out += oy
        return YPosVariable(out)



great, put these variables in your tracker class file ;)

qgeissmann · 2017-11-14T17:29:29Z

src/ethoscope/trackers/adaptive_bg_tracker.py

+        return [out]
+
+
+class AdaptiveBGModelExtraObjectPosInfo(AdaptiveBGModel):


let's make another file for this one class

qgeissmann · 2017-11-14T17:29:56Z

src/ethoscope/drawers/drawers.py

                cv2.ellipse(img,((pos["x"],pos["y"]), (pos["w"],pos["h"]), pos["phi"]),colour,1, LINE_AA)
+
+
+class SubRoiDrawer(BaseDrawer):


we should put your new drawer in another file ;)

…ecribe the subrois in which a fly stays in every frame. Also, the subroi drawer was put in a new file

…groundSubstractor, correction for find subroi

nazabic added 4 commits November 3, 2017 13:14

Set up the interpolation such that there is no modifications of pixel…

accd3f4

…s values after the affine transformation

Code working fine except for a few border pixels

82ea671

new variable saved in the database that contains the grayscale region…

4b73c7c

… in of the position of the fly on the mask.

Make sure the roi's regions size and type is equal to the mask size a…

8279e08

…nd type, otherwise regions = mask and throw exceptions

qgeissmann approved these changes Nov 7, 2017

View reviewed changes

qgeissmann requested changes Nov 7, 2017

View reviewed changes

nazabic added 4 commits November 8, 2017 18:07

Requested changes at pull request

0a84df7

Formatring correction

18cf9d2

More formatring correction

5160372

Changed name of argument to match the rest of the code

baf0cd6

qgeissmann approved these changes Nov 10, 2017

View reviewed changes

nazabic added 3 commits November 14, 2017 15:55

Changes to pull request and customized tracker and drawer for the gra…

27ff078

…y subrois.

Adding the total number of pixels of the fly at each frame in the dat…

2a69173

…abase, and a few name refactorings.

Forgotten comma

0954500

qgeissmann approved these changes Nov 14, 2017

View reviewed changes

nazabic added 15 commits November 15, 2017 10:24

Put the new tracker in a new file along with the new variables that d…

5590db7

…ecribe the subrois in which a fly stays in every frame. Also, the subroi drawer was put in a new file

Remove some spaces and one import

27daa55

Make separate file for new roi builder

b311ed1

Make it opencv3 compatible, add new prototype for tracking using Back…

cec0c17

…groundSubstractor, correction for find subroi

Make it opencv3 compatible, add new prototype for tracking using Back…

0f97318

…groundSubstractor, correction for find subroi

random colors for each fly

c88b323

modifications

0db573a

Mess so far

deb027d

Mess so far

7c0c097

separates correctly the contours, first try

a6a23be

separates correctly the contours, first try

fc81891

start of multi tracking refactoring

242dbdf

start of multi tracking refactoring

c22518b

Multi tracking with ids almost working

b403751

Multi tracking working with kmeans

e35f82e

Tracking working fine

b464a49

ggilestro closed this Jul 1, 2020

		return [out]


		class AdaptiveBGModelExtraObjectPosInfo(AdaptiveBGModel):

		cv2.ellipse(img,((pos["x"],pos["y"]), (pos["w"],pos["h"]), pos["phi"]),colour,1, LINE_AA)


		class SubRoiDrawer(BaseDrawer):

Adds new variable that outputs the gray value corresponding to the position of the fly in the grayscale mask #84

Adds new variable that outputs the gray value corresponding to the position of the fly in the grayscale mask #84

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nazabic commented Nov 7, 2017

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qgeissmann Nov 7, 2017 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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qgeissmann Nov 7, 2017 •

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