Inv scanimage#1
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Created the java class ScannImageTiffReader
I wrote down the basic necessary functions and starting implementing them where possible.
Added the isSingleFile function to check for the LOCI hack .xml metadata file that contains info like the pixel size.
Started to implement the getSeriesUsedFiles function and to use the PrairieReader as a reference for how to implement the xml file.
Using warnings rather than exception means that the validateOMEXML itself will handle logger statements for validation failures and also covers XMLTools warnings
Handle NaN values in FormatTools.getStagePosition()
Add format page for SPE
Add SPC FIFO format page
…to inv---ScanImage
Update version history for m5
The basic metadata parsing for IsThisType and XYZCT is now working.
Started implementing suffix check. Not completed.
Added the PC path correctly and made a println statement for a warning message that will need to be removed
…to inv---ScanImage
Added a singleTiffMode trigger to the suffix parsing logic.
Separated the main function into a new test file to reduce software bloat and to enable the logger.
Implemented logic to allow the reader to warn in case there is a suffix due to an _ in the filename, but where the suffix is a string and not an integer as expected.
Implemented getSeriesUsedFiles, including a to-be-deleted temporary else block that tests out the results in initStandardMetadata
The reader now checks to see that the actual number of channels correctly corresponds to the number of channels in the metadata. It issues a warning if it is not correct, but currently does nothing else.
I removed the code that caused the metadata reader to run twice, and realized that the channel reading is still bugged.
Added comments with Curtis' name in them for him to find certain lines of code
The channle checking mechanism is now fixed. The base tiff reader reads in channels as the T dimension form a ScanImage file.
Added ScanImageTiffReader to the standard ImageReader, so now you can all just the ImageReader rather than the ScanImageTiffReader by itself
the function getSeriesUsedFiles now properly checks for the existence of files that it should expect based on the metadata. If it doesn't find them it turns on singleTiffMode and returns a list that is the single file.
Started converting the references from xml to txt
I added functionality to search for a txt file and read it in. If the first line has FOV = Value, then it records a key value pair of "FOV" and "Value". This is the first step to calulating the actual pixel dimensions.
I added a series of functions across the program to test for the correct metadata file, find the X and Y resolutions based on that metadata file. I also straight up took the key from the Z resolution line in the Scan Image comment and turned it into the global variable. This was applied in metadata store. None of this was tested.
I troubleshooted and fixed the X, Y, and Z resolution setters. I didn't directly access the store, but I made sure the values were correct and we were getting into the right loops.
Changed the metadata and its readers to read in pixel resolution rather than field of view. If we need to do field of view, remember to convert it to pixel width before putting it into the store.
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