search

henrypinkard / Pygellan

[DEPREACATED] Python interface for data-driven microscopy with Micro-manager/Micro-Magellan
BSD 3-Clause "New" or "Revised" License
14 stars 3 forks source link

MM 2.2.0 No metadata #16

Closed kdmarchuk closed 4 years ago

kdmarchuk commented 4 years ago

Using the demo config for acquisitions and explore, no XML metadata file is produced.

henrypinkard commented 4 years ago

You mean the FIJI_BigDataViewer_Metadata.xml file? I took this out because it no longer had a function

kdmarchuk commented 4 years ago

Imaricumpiler is crashing on test datasets. FIJI has been recently updated. I had assumed it was the lack of xml.

Can't find display settings in file: test_MagellanStack.tif Num channels tag missiing java.lang.RuntimeException at org.micromanager.plugins.magellan.misc.MD.getNumChannels(MD.java:563) at org.micromanager.plugins.magellan.imagedisplay.DisplaySettings.getDisplaySettingsFromSummary(DisplaySettings.java:46) at org.micromanager.plugins.magellan.acq.TaggedImageStorageMultipageTiff.processSummaryMD(TaggedImageStorageMultipageTiff.java:113) at org.micromanager.plugins.magellan.acq.TaggedImageStorageMultipageTiff.setSummaryMetadata(TaggedImageStorageMultipageTiff.java:390) at org.micromanager.plugins.magellan.acq.TaggedImageStorageMultipageTiff.openExistingDataSet(TaggedImageStorageMultipageTiff.java:167) at org.micromanager.plugins.magellan.acq.TaggedImageStorageMultipageTiff.(TaggedImageStorageMultipageTiff.java:91) at MM.MMDataset.(MMDataset.java:163) at pipeline.God.fileToLoadedMMData(God.java:108) at pipeline.God$2.run(God.java:128) at java.lang.Thread.run(Thread.java:748)

Num channels tag missiing

henrypinkard commented 4 years ago

This is neither a bug in Pygellan nor Magellan. I removed that metadata tag a couple months ago when doing a refactor to make acquisitions more flexible with respect to channels. You no longer know the number of channels in advance, rather they are just added at runtime. This allows for on the fly adding and deleting of channels, a necessary modification for flexible acquisition control I will add in future versions.

This means that the imaricumpiler source code would need to be updated to read the number of channels directly from the image tags. There is a new function that provides the same information that you would need replace the offending line (MMDataset.java:163) with.