Error messages should be more informative (pipeline_demo.py)

[chuong]

I tried the latest script today but got a many error messages complaining missing inputs even though these inputs are provided in pipeline.yml and timestream.yml:

$ python pipeline_demo.py  -i /home/chuong/Data/phenocam/a_data/TimeStreams/Borevitz/BVZ0036/BVZ0036-GC05R-C01~fullres-orig -o /home/chuong/Data/phenocam/a_data/TimeStreams/Borevitz/BVZ0036/BVZ0036-GC05R-C01~fullres-chuong-test
pipeline._9.mess=---Writing Features---
pipeline._9.name=writefeatures_csv
pipeline._8.mess=---Extract Plant Features---
pipeline._8.name=featureextract
pipeline._8.features=['all']
pipeline._7.mess=---Writing Image---
pipeline._7.name=imagewrite
pipeline._7.outstream=segg
pipeline._6.mess=---Performing plant segmentation---
pipeline._6.methargs={'threshold': 0.6, 'kSize': 5, 'blobMinSize': 50}
pipeline._6.name=plantextract
pipeline._6.method=method1
pipeline._5.potFile=Pot.png
pipeline._5.name=potdetect
pipeline._5.mess=---Perform pot detection---
pipeline._5.potPositions=[3075.7731696472, 1555.6248980913108]
pipeline._5.potSize=[271, 278]
pipeline._5.potTemplateFile=PotTemplate.png
pipeline._5.traySize=[1155, 1369]
pipeline._4.trayFiles=Tray_%02d.png
pipeline._4.name=traydetect
pipeline._4.mess=---Perform tray detection---
pipeline._4.trayNumber=8
pipeline._4.settingPath=_data
pipeline._4.trayPositions=[[769.8614778705123, 2459.8952985945198], [1983.3218079445069, 2477.086304095753], [3226.049545720228, 2481.143605746123], [4448.643579645086, 2499.29641014711], [768.3232767702657, 1016.2193047062192], [1994.4364112452467, 999.5856008553558], [3223.0877468204744, 1007.1429025057257], [4446.624479094962, 1013.2384052563424]]
pipeline._3.mess=---Write image---
pipeline._3.name=imagewrite
pipeline._3.outstream=corr
pipeline._2.mess=---Perform color correction---
pipeline._2.minIntensity=15
pipeline._2.name=colorcorrect
pipeline._1.mess=---Perform color card detection---
pipeline._1.colorcardFile=CapturedColorcard.png
pipeline._1.colorcardPosition=[2763.8665252432197, 1578.0483581906267]
pipeline._1.colorcardTrueColors=[[115.0, 196.0, 91.0, 94.0, 129.0, 98.0, 223.0, 58.0, 194.0, 93.0, 162.0, 229.0, 49.0, 77.0, 173.0, 241.0, 190.0, 0.0, 242.0, 203.0, 162.0, 120.0, 84.0, 50.0], [83.0, 147.0, 122.0, 108.0, 128.0, 190.0, 124.0, 92.0, 82.0, 60.0, 190.0, 158.0, 66.0, 153.0, 57.0, 201.0, 85.0, 135.0, 243.0, 203.0, 163.0, 120.0, 84.0, 50.0], [68.0, 127.0, 155.0, 66.0, 176.0, 168.0, 47.0, 174.0, 96.0, 103.0, 62.0, 41.0, 147.0, 71.0, 60.0, 25.0, 150.0, 166.0, 245.0, 204.0, 162.0, 120.0, 84.0, 52.0]]
pipeline._1.name=colorcarddetect
pipeline._0.imageSize=[5184, 3456]
pipeline._0.mess=---Perform optical undistortion---
pipeline._0.cameraMatrix=[[4234.949389, 0.0, 2591.5], [0.0, 4234.949389, 1727.5], [0.0, 0.0, 1.0]]
pipeline._0.rotationAngle=180.0
pipeline._0.distortCoefs=[-0.166191, 0.142034, 0.0, 0.0, 0.0]
pipeline._0.name=undistort
outstreams._1.name=corr
outstreams._0.name=segg
general.endHourRange.second=0
general.endHourRange.minute=0
general.endHourRange.hour=15
general.startDate.hour=9
general.startDate.month=6
general.startDate.second=0
general.startDate.year=2014
general.startDate.day=18
general.startDate.minute=0
general.timeInterval=900
general.visualise=False
general.startHourRange.second=0
general.startHourRange.minute=0
general.startHourRange.hour=9

Timestream instance created:
   ts.path: /home/chuong/Data/phenocam/a_data/TimeStreams/Borevitz/BVZ0036/BVZ0036-GC05R-C01~fullres-orig
   ts.name: BVZ0036-GC05R-C01~fullres-orig
   ts.version: 1
   ts.start_datetime: 2014-06-18 18:30:00
   ts.end_datetime: 2014-08-06 07:30:00
   ts.image_type: jpg
   ts.extension: JPG
   ts.interval: 1800
Traceback (most recent call last):
  File "pipeline_demo.py", line 146, in <module>
    pl = pipeline.ImagePipeline(plConf.pipeline, ctx)
  File "/home/chuong/Workspace/timestreamlib/timestream/manipulate/pipeline.py", line 73, in __init__
    self.pipeline.append( component(context, **setElem) )
  File "/home/chuong/Workspace/timestreamlib/timestream/manipulate/pipecomponents.py", line 173, in __init__
    super(ColorCardDetector, self).__init__(**kwargs)
  File "/home/chuong/Workspace/timestreamlib/timestream/manipulate/pipecomponents.py", line 62, in __init__
    raise PCExBadRunExpects(self.__class__)
timestream.manipulate.pipecomponents.PCExBadRunExpects: PipeComp_Error: The call to colorcarddetect should consider 
  colorcarddetect
  (Initializing Args)
    minIntensity(optional): Skip colorcard detection if intensity below this value
    mess(required): Detect color card
    colorcardTrueColors(required): Matrix representing the groundtrue color card colors
    colorcardFile(required): Path to the color card file
    settingPath(required): Path to setting files
    colorcardPosition(required): (x,y) of the colorcard
  (Args Received)
    <class 'timestream.TimeStreamImage'>
  (Args Returned)
    <class 'timestream.TimeStreamImage'>
    <type 'list'>

$

[kdm9]

Chuong,

please use backticks around any copy-pasing:

paste code

goes nicely to:

paste code

I fixed you bug report here, it's now a lot easier on the eyes.

Cheers, K

[Joelgranados]

chuong can you paste your configuration files? I'll try to reproduce on my end.

[chuong]

Here is the content of timestream.yml for BVZ0036-GC05R-C01~fullres-orig:

colorcarddetect:
  colorcardFile: CapturedColorcard.png
  colorcardPosition: [2763.8665252432197, 1578.0483581906267]
  colorcardTrueColors:
  - [115.0, 196.0, 91.0, 94.0, 129.0, 98.0, 223.0, 58.0, 194.0, 93.0, 162.0, 229.0,
    49.0, 77.0, 173.0, 241.0, 190.0, 0.0, 242.0, 203.0, 162.0, 120.0, 84.0, 50.0]
  - [83.0, 147.0, 122.0, 108.0, 128.0, 190.0, 124.0, 92.0, 82.0, 60.0, 190.0, 158.0,
    66.0, 153.0, 57.0, 201.0, 85.0, 135.0, 243.0, 203.0, 163.0, 120.0, 84.0, 50.0]
  - [68.0, 127.0, 155.0, 66.0, 176.0, 168.0, 47.0, 174.0, 96.0, 103.0, 62.0, 41.0,
    147.0, 71.0, 60.0, 25.0, 150.0, 166.0, 245.0, 204.0, 162.0, 120.0, 84.0, 52.0]
colorcorrect: {minIntensity: 15}
plantextract:
  methargs: {blobMinSize: 50, kSize: 5, threshold: 0.6}
  method: method1
potdetect:
  potFile: Pot.png
  potPositions: [3075.7731696472, 1555.6248980913108]
  potSize: [271, 278]
  potTemplateFile: PotTemplate.png
  traySize: [1155, 1369]
traydetect:
  settingPath: _data
  trayFiles: Tray_%02d.png
  trayNumber: 8
  trayPositions:
  - [769.8614778705123, 2459.8952985945198]
  - [1983.3218079445069, 2477.086304095753]
  - [3226.049545720228, 2481.143605746123]
  - [4448.643579645086, 2499.29641014711]
  - [768.3232767702657, 1016.2193047062192]
  - [1994.4364112452467, 999.5856008553558]
  - [3223.0877468204744, 1007.1429025057257]
  - [4446.624479094962, 1013.2384052563424]
undistort:
  cameraMatrix:
  - [4234.949389, 0.0, 2591.5]
  - [0.0, 4234.949389, 1727.5]
  - [0.0, 0.0, 1.0]
  distortCoefs: [-0.166191, 0.142034, 0.0, 0.0, 0.0]
  imageSize: [5184, 3456]
  rotationAngle: 180.0

[Joelgranados]

Can you also paste the pipeline.yml

[chuong]

Sorry I am at home now so I don't access to the folder. The pipeline.yml is in the folder /mnt/phenocam/a_data/TimeStreams/Borevitz/BVZ0036/BVZ0036-GC05R-C01~fullres-orig/_data

This file should be quite the similar to other pipeline.yml of this experiment

[chuong]

I found that some sections of my timestream.yml don't have settingPath entry so I add this. Another problem with my timestream.yml is the mispelling of method: method1, instead of `meth: method1. These are all fixed now. The error message needs to be more informative to locate the source of the error.

Now I have potdetection error which is an unrelated to the reported issues

[Joelgranados]

Re-opening so we get better at producing error messages

[chuong]

I just made a change to PCExBadRunExpects to make the error message more informative.

[chuong]

To reproduce the error, just randomly remove some entries from a working pipeline.yml or timestream.yml.

[Joelgranados]

Closing, seems Chuong took care of it :)