FlagImage doesn't respect individual flag's 'Skip image set' settings

[bethac07]

@minh-doan was running a pipeline where FlagImage was set as below- the first flag, QCFlag_empty, had Skip image set if flagged?:Yes, but the second flag, QCFlag_bright_artifact, had Skip image set if flagged?:No. Looking at an example of a CSV that failed QC and the downstream steps were skipped, I noticed this:

Metadata_QCFlag_bright_artifact,1
Metadata_QCFlag_empty,0

This image failed bright_artifact but NOT empty, but was skipped anyway. My guess is that if any flag has Skip image set if flagged?:Yes, it skips whenever any flag is triggered, but I haven't rigorously proven that yet.

---

FlagImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Hidden:2
    Hidden:1
    Name the flag\'s category:Metadata
    Name the flag:QCFlag_empty
    How should measurements be linked?:Flag if any fail
    Skip image set if flagged?:Yes
    Flag is based on:Rules
    Select the object to be used for flagging:None
    Which measurement?:ImageQuality_PercentMaximal_OrigDNA
    Flag images based on low values?:No
    Minimum value:0
    Flag images based on high values?:Yes
    Maximum value:0.25
    Rules file location:Elsewhere...\x7C/home/ubuntu/bucket/projects/2016_12_07_HepG2_Janssen/workspace/pipelines/
    Rules file name:rules.txt
    Class number:2
    Hidden:1
    Name the flag\'s category:Metadata
    Name the flag:QCFlag_bright_artifact
    How should measurements be linked?:Flag if any fail
    Skip image set if flagged?:No
    Flag is based on:Rules
    Select the object to be used for flagging:None
    Which measurement?:None
    Flag images based on low values?:Yes
    Minimum value:0
    Flag images based on high values?:Yes
    Maximum value:1
    Rules file location:Elsewhere...\x7C/home/ubuntu/bucket/projects/2016_12_07_HepG2_Janssen/workspace/pipelines/
    Rules file name:rules.txt
    Class number:3

[braymp]

There's a How should measurements be linked? setting, which is set to Flag if any fail which is set to Yes here. With this combo of settings, if any fail, the flag is set, and if the flag is set, the image set is skipped.

This should only matter if multiple measurements within the same flag are used, but I wonder if it might be that this setting is being incorrectly applied across multiple flags as well (i.e., a bug)?

[braymp]

Also, I can never remember whether a value of 0 means it passed or failed QC; the documentation is a bit confusing (even though I probably wrote it) 😄

So, obvious question: Are you sure you have the meaning of the flag value correct?

[bethac07]

0 is supposed to mean passes QC, because there are 0 Flags- if I look at the Image_Metadata from a CSV in the same plate that did process fully, both Metadata_QC columns are set to 0, so I'm reasonably certain I have that right. It definitely doesn't hurt to check though 😄

[bethac07]

Also, I think you're too hard on your documentation skillz, this seems pretty clear to me!

The value of the flag is 1 if the image meets the selected criteria (for example, if it fails QC), and 0 if it does not meet the criteria (if it passes QC).