Lots of warnings at start of execution

[Joelgranados]

While running

python pipeline_demo.py -i /mnt/phenocam/a_data/TimeStreams/Borevitz/BVZ0036/BVZ0036-GC02L-C01~fullres-orig/

from the virtual environment /home/joel/.virtualenvs/timestreamlib/ it seems to always miss the 0 tray. Here is the output of the normal execution:

Process /mnt/phenocam/a_data/TimeStreams/Borevitz/BVZ0036/BVZ0036-GC02L-C01~fullres-orig/2014/2014_06/2014_06_08/2014_06_08_11/BVZ0036-GC02L-C01~fullres-orig_2014_06_08_11_45_00_00.JPG ...
Time stamp 2014-06-08 11:45:00
---perform optical undistortion---
---perform color card detection---
Cannot find color card
---perform color correction---
Skip color correction
---Write image---
---perform tray detection---
Urecoverable error at traydetect: Low tray matching score. Likely tray 0 is missing.

Any ideas????

[Joelgranados]

It finally started to produce some data after a long set of errors. Here is the first image that got detected:

Missing Image
Process /mnt/phenocam/a_data/TimeStreams/Borevitz/BVZ0036/BVZ0036-GC02L-C01~fullres-orig/2014/2014_06/2014_06_18/2014_06_18_09/BVZ0036-GC02L-C01~fullres-orig_2014_06_18_09_00_00_00.JPG ...
Time stamp 2014-06-18 09:00:00
---perform optical undistortion---
---perform color card detection---
/home/joel/.virtualenvs/timestreamlib/local/lib/python2.7/site-packages/timestream-0.1a2-py2.7.egg/timestream/manipulate/correct_detect.py:393: RuntimeWarning: invalid value encountered in power
/home/joel/.virtualenvs/timestreamlib/local/lib/python2.7/site-packages/timestream-0.1a2-py2.7.egg/timestream/manipulate/correct_detect.py:391: RuntimeWarning: invalid value encountered in power
/home/joel/.virtualenvs/timestreamlib/local/lib/python2.7/site-packages/scipy/optimize/minpack.py:419: RuntimeWarning: Number of calls to function has reached maxfev = 10000.
  warnings.warn(errors[info][0], RuntimeWarning)
---perform color correction---
/home/joel/.virtualenvs/timestreamlib/local/lib/python2.7/site-packages/timestream-0.1a2-py2.7.egg/timestream/manipulate/correct_detect.py:427: RuntimeWarning: invalid value encountered in power
/home/joel/.virtualenvs/timestreamlib/local/lib/python2.7/site-packages/timestream-0.1a2-py2.7.egg/timestream/manipulate/pipecomponents.py:255: RuntimeWarning: invalid value encountered in less
/home/joel/.virtualenvs/timestreamlib/local/lib/python2.7/site-packages/timestream-0.1a2-py2.7.egg/timestream/manipulate/pipecomponents.py:256: RuntimeWarning: invalid value encountered in greater
---Write image---
---perform tray detection---
---perform pot detection---
---Performing plant segmentation---
---Writing Image---
---extracting features---
---Writing Features---
Done
Process /mnt/phenocam/a_data/TimeStreams/Borevitz/BVZ0036/BVZ0036-GC02L-C01~fullres-orig/2014/2014_06/2014_06_18/2014_06_18_09/BVZ0036-GC02L-C01~fullres-orig_2014_06_18_09_15_00_00.JPG ...
Time stamp 2014-06-18 09:15:00

[chuong]

Not sure why it has problem detecting tray 0 but images of BVZ0036-GC02L-C01 don't have color card before 2014-06-18.

[kdm9]

This is (kindof) a duplicate of #83. Closing

[Joelgranados]

Nope, the two issues are different.

These error messages only appear at the beginning of the execution and are definitely not produced by raise PCExBadRunExpects(self.__class__, attrKey) like in 83. please keep open.

[kdm9]

OK, my bad.

[Joelgranados]

I found this at timestream/manipulate/correct_detect.py#L468. When we do a np.power(TempRGB[0, :]/255.0, ColorGamma[0]) and the base is a negative number. The result is 0 but a warning is thrown.

[Joelgranados]

And we pass a ColorMatrix with negative numbers as part of the least square approximation of the intermediate values in the color correction component. What we should do here is ignore these warnings....

[Joelgranados]

There are more:

1. There is another one at timestream/manipulate/correct_detect.py#L526, but am unsure if we should ignore it. This one is the same power problems as described above but is not part of a least square search.
2. There is another in pipecomponents.py:ImageColorCorrector.call: "self.imageCorrected < 0". It warns once in this line. Still unsure why.

This bug requires a bit more exploration.

[Joelgranados]

This is my updated warning output:

17:04:06: ---Perform color card detection---
/usr/lib/python2.7/dist-packages/scipy/optimize/minpack.py:418: RuntimeWarning: Number of calls to function has reached maxfev = 10000.
  warnings.warn(errors[info][0], RuntimeWarning)
17:04:06: ---Perform color correction---
/home/joel/.virtualenvs/timestreamlib/local/lib/python2.7/site-packages/timestream-e9a59eb_dirty-py2.7.egg/timestream/manipulate/correct_detect.py:529: RuntimeWarning: invalid value encountered in power
  CorrectedRGB[0, :] = 255.0*np.power(TempRGB[0, :]/255.0, ColorGamma[0])
/home/joel/.virtualenvs/timestreamlib/local/lib/python2.7/site-packages/timestream-e9a59eb_dirty-py2.7.egg/timestream/manipulate/correct_detect.py:535: RuntimeWarning: invalid value encountered in less
  CorrectedR[np.where(CorrectedR < 0)] = 0
/home/joel/.virtualenvs/timestreamlib/local/lib/python2.7/site-packages/timestream-e9a59eb_dirty-py2.7.egg/timestream/manipulate/correct_detect.py:538: RuntimeWarning: invalid value encountered in greater
  CorrectedR[np.where(CorrectedR > 255)] = 255
/home/joel/.virtualenvs/timestreamlib/local/lib/python2.7/site-packages/timestream-e9a59eb_dirty-py2.7.egg/timestream/manipulate/pipecomponents.py:323: RuntimeWarning: invalid value encountered in less
  self.imageCorrected[np.where(self.imageCorrected < 0)] = 0
/home/joel/.virtualenvs/timestreamlib/local/lib/python2.7/site-packages/timestream-e9a59eb_dirty-py2.7.egg/timestream/manipulate/pipecomponents.py:324: RuntimeWarning: invalid value encountered in greater
  self.imageCorrected[np.where(self.imageCorrected > 255)] = 255
17:04:13: ---Perform tray detection---

Look for the RuntimeWarning...