Developer Interface¶
This part of the documentation covers the interfaces of LLSpy that one might use in development or interactive sessions. This page is a work in progress: there is much more undocumented functionality in the source code.
Main Functions¶
Processing routines can be called directly with a path to the LLS experiment directory.
Main Classes¶
Most routines in LLSpy begin with the instantiation of an LLSdir object.
This class is also instantiated by the preview and process functions
LLS directory¶
cudaDeconv wrapper¶
*Settings.txt parser¶
Wrapped CUDA functions¶
Exceptions¶
Schema¶
Many functions such as the preview and process functions accept keyword
arguments that determine processing options. These are all validated using the schema
in llspy.schema. Options include:
| Key | Default | Description |
|---|---|---|
| correctFlash | False | do Flash residual correction |
| moveCorrected | True | move processed corrected files to original LLSdir |
| flashCorrectTarget | cpu | {“cpu”, “cuda”, “parallel”} for FlashCor |
| medianFilter | False | do Keller median filter |
| keepCorrected | False | save corrected images after processing |
| trimZ | (0, 0) | num Z pix to trim off raw data before processing |
| trimY | (0, 0) | num Y pix to trim off raw data before processing |
| trimX | (0, 0) | num X pix to trim off raw data before processing |
| nIters | 10 | deconvolution iters |
| nApodize | 15 | num pixels to soften edge with for decon |
| nZblend | 0 | num top/bot Z sections to blend to reduce axial ringing |
| bRotate | False | do Rotation to coverslip coordinates |
| rotate | None | angle to use for rotation |
| saveDeskewedRaw | False | whether to save raw deskewed |
| saveDecon | True | whether to save decon stacks |
| MIP | (0, 0, 1) | whether to save XYZ decon MIPs |
| rMIP | (0, 0, 0) | whether to save XYZ raw MIPs |
| mergeMIPs | True | do MIP merge into single file (decon) |
| mergeMIPsraw | True | do MIP merge into single file (deskewed) |
| uint16 | True | save decon as unsigned int16 |
| uint16raw | True | save deskewed raw as unsigned int16 |
| bleachCorrection | False | do photobleach correction |
| doReg | False | do channel registration |
| regRefWave | 488 | reference wavelength when registering |
| regMode | 2step | transformation mode when registering |
| regCalibPath | None | directory with registration calibration data |
| mincount | 10 | minimum number of beads expected in regCal data |
| reprocess | False | reprocess already-done data when processing |
| tRange | None | time range to process (None means all) |
| cRange | None | channel range to process (None means all) |
| otfDir | None | directory to look in for PSFs/OTFs |
| camparamsPath | None | file path to camera Parameters .tif |
| verbose | 0 | verbosity level when processing {0,1,2} |
| cropMode | none | {manual, auto, none} - auto-cropping based on image content |
| autoCropSigma | 2 | gaussian blur sigma when autocropping |
| width | 0 | final width when not autocropping (0 = full) |
| shift | 0 | crop shift when not autocropping |
| cropPad | 50 | additional pixels to keep when autocropping |
| background | -1 | background to subtract. -1 = autodetect |
| compressRaw | False | do compression of raw data after processing |
| compressionType | lbzip2 | compression binary {lbzip2, bzip2, pbzip2, pigz, gzip} |
| writeLog | True | write settings to processinglog.txt |