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Added support for logging #50

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Added support for logging #50

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Commits on Apr 11, 2024

  1. limit read and compute blocks transforms

    Cristian Goina committed Apr 11, 2024
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  2. only throttle compute transforms

    Cristian Goina committed Apr 11, 2024
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  3. blocks may have not been dispatched in the correct order to compute b… 

    …lock transform, so now I am reading all corresponding blocks in the same method and return them as dask arrays
    Cristian Goina committed Apr 11, 2024
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  4. allow null masks

    Cristian Goina committed Apr 11, 2024
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  5. abstract out block reading as dask array

    Cristian Goina committed Apr 11, 2024
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  6. trying to figure out the fancy indexing not supported error

    Cristian Goina committed Apr 11, 2024
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  7. pass params as dask arrays

    Cristian Goina committed Apr 11, 2024
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  8. create dask array only if it's not already one

    Cristian Goina committed Apr 11, 2024
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  9. use vindex for daskarrays

    Cristian Goina committed Apr 11, 2024
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  10. compute the image first

    Cristian Goina committed Apr 11, 2024
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Commits on Apr 12, 2024

  1. compute blocks before they are passed to the alignment pipeline to av… 

    …oid the fancy indexing error
    Cristian Goina committed Apr 12, 2024
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  2. comment

    Cristian Goina committed Apr 12, 2024
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Commits on Apr 16, 2024

  1. factored out throttle method and use it in other distributed calls as… 

    … well
    Cristian Goina committed Apr 16, 2024
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  2. missed file from commit

    Cristian Goina committed Apr 16, 2024
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Commits on Apr 17, 2024

  1. return inverse block as dask array

    Cristian Goina committed Apr 17, 2024
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  2. the write seems to be invoked before the invert completes, so I am tr… 

    …ying to see how I can force execution
    Cristian Goina committed Apr 17, 2024
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Commits on Apr 18, 2024

  1. fix error - var was used before declared

    Cristian Goina committed Apr 18, 2024
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  2. trying to get the result only when needed to see if it manages space … 

    …better
    Cristian Goina committed Apr 18, 2024
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  3. compute block before writing it

    Cristian Goina committed Apr 18, 2024
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  4. do not return block to eliminate stale file handle error

    Cristian Goina committed Apr 18, 2024
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  5. return futures with results

    Cristian Goina committed Apr 18, 2024
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  6. typo

    Cristian Goina committed Apr 18, 2024
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Commits on Apr 19, 2024

  1. write align results (reduce) in the driver

    Cristian Goina committed Apr 19, 2024
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  2. fix the expect da error by computing the block before writing it

    Cristian Goina committed Apr 19, 2024
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  3. extract result only right before writing

    Cristian Goina committed Apr 19, 2024
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Commits on Apr 20, 2024

  1. removed the use of dask arrays + debug message

    Cristian Goina committed Apr 20, 2024
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  2. no dask array used so no need to compute

    Cristian Goina committed Apr 20, 2024
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  3. write inverted result in the driver when collecting the results

    Cristian Goina committed Apr 20, 2024
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Commits on Apr 24, 2024

  1. removed debug message

    Cristian Goina committed Apr 24, 2024
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Commits on Apr 29, 2024

  1. write voxel spacing in the displacement vector

    Cristian Goina committed Apr 29, 2024
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  2. changed how the block is updated

    Cristian Goina committed Apr 29, 2024
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  3. default bigstream config

    Cristian Goina committed Apr 29, 2024
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Commits on Apr 30, 2024

  1. add voxel spacing args in case they are not available

    Cristian Goina committed Apr 30, 2024
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  2. renamed or added flags to follow the convention <global|local>-<arg>

    Cristian Goina committed Apr 30, 2024
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  3. convert voxel spacing arg to np array

    Cristian Goina committed Apr 30, 2024
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Commits on May 2, 2024

  1. changed parameters to be able to pass in all align params in a yaml f… 

    …ile; a default configuration is available as source code
    Cristian Goina committed May 2, 2024
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  2. print timestamp with configure irm args

    Cristian Goina committed May 2, 2024
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  3. bump up version because of the yaml config

    Cristian Goina committed May 2, 2024
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  4. added default yaml config to resources to have it as a reference

    Cristian Goina committed May 2, 2024
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  5. print global transform file

    Cristian Goina committed May 2, 2024
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  6. changed text

    Cristian Goina committed May 2, 2024
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Commits on May 3, 2024

  1. fixed the dimensions for transform voxel spacing params

    Cristian Goina committed May 3, 2024
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  2. added an ImageData type to be able to read image blocks from large ti… 

    …ffs without reading entire image
    Cristian Goina committed May 3, 2024
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  3. option to pass voxel spacing to deform

    Cristian Goina committed May 3, 2024
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  4. parameter for transform spacing

    Cristian Goina committed May 3, 2024
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Commits on May 7, 2024

  1. changes so that we could handle empty inputs such as empty global inp… 

    …uts and/or empty local inputs
    Cristian Goina committed May 7, 2024
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  2. changes to transform spacing

    Cristian Goina committed May 7, 2024
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  3. fixed error caused by the mask shape

    Cristian Goina committed May 7, 2024
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  4. fix transform spacing

    Cristian Goina committed May 7, 2024
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Commits on May 8, 2024

  1. set voxel spacing for mov image same as fix voxel spacing

    Cristian Goina committed May 8, 2024
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  2. remove defaults channel

    Cristian Goina committed May 8, 2024
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  3. print attributes

    Cristian Goina committed May 8, 2024
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  4. Set attrs for zarr too

    Cristian Goina committed May 8, 2024
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Commits on May 9, 2024

  1. handle null downsampling values instead of null set it to 1

    Cristian Goina committed May 9, 2024
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  2. put deform spacing in different order

    Cristian Goina committed May 9, 2024
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  3. Check for none instead of using the simple not - it didn't work as I … 

    …expected it for numpy arrays
    Cristian Goina committed May 9, 2024
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  4. changed debug message

    Cristian Goina committed May 9, 2024
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  5. only write valid values

    Cristian Goina committed May 9, 2024
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Commits on May 10, 2024

  1. fix check for image_downsampling

    Cristian Goina committed May 10, 2024
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Commits on May 12, 2024

  1. use 1 for affine spacing instead of None

    Cristian Goina committed May 12, 2024
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Commits on May 13, 2024

  1. debug messages

    Cristian Goina committed May 13, 2024
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  2. debug messages

    Cristian Goina committed May 13, 2024
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  3. catch exception in transform block

    Cristian Goina committed May 13, 2024
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  4. print block coords

    Cristian Goina committed May 13, 2024
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  5. more print outs

    Cristian Goina committed May 13, 2024
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  6. syntax error

    Cristian Goina committed May 13, 2024
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  7. fixes for transform spacing

    Cristian Goina committed May 13, 2024
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Commits on May 14, 2024

  1. Merge branch 'master' into goinac-dev

    Cristian Goina committed May 14, 2024
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  2. set safeguard exc to false for local ransac

    Cristian Goina committed May 14, 2024
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Commits on May 17, 2024

  1. minor comment change

    Cristian Goina committed May 17, 2024
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  2. changed reading voxel_spacing

    Cristian Goina committed May 17, 2024
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  3. remove global transform main script

    Cristian Goina committed May 17, 2024
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  4. more messing with the axis for voxel spacing

    Cristian Goina committed May 17, 2024
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  5. more changes to get the deform axes right

    Cristian Goina committed May 17, 2024
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  6. returned voxel spacing property was not reversed

    Cristian Goina committed May 17, 2024
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Commits on May 21, 2024

  1. Merge branch 'master' into goinac-dev

    Cristian Goina committed May 21, 2024
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  2. support for mask descriptors that could be list or tuple of values

    Cristian Goina committed May 21, 2024
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Commits on May 30, 2024

  1. fixed pixel attributes

    Cristian Goina committed May 30, 2024
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Commits on May 31, 2024

  1. made some changes to see if I can get the same deform vector

    Cristian Goina committed May 31, 2024
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Commits on Jun 6, 2024

  1. separate main drivers for local and global registration; option to re… 

    …ad the steps from the bigstream.config
    Cristian Goina committed Jun 6, 2024
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Commits on Jun 8, 2024

  1. fixed transform shape when coming from yaml

    Cristian Goina committed Jun 8, 2024
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Commits on Jun 10, 2024

  1. option to put the alignment in a different location than the transform

    Cristian Goina committed Jun 10, 2024
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  2. different args for the transformation location and the result of appl… 

    …ying the transformation; the default output can be used if one wants to use the same location for both
    Cristian Goina committed Jun 10, 2024
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  3. mask blocks for tuple masks too

    Cristian Goina committed Jun 10, 2024
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  4. fixed a NPE

    Cristian Goina committed Jun 10, 2024
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  5. print foreground ratio

    Cristian Goina committed Jun 10, 2024
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  6. syntax error

    Cristian Goina committed Jun 10, 2024
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Commits on Jun 13, 2024

  1. changed print out

    Cristian Goina committed Jun 13, 2024
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Commits on Jun 14, 2024

  1. fixed arg for apply global transform

    Cristian Goina committed Jun 14, 2024
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  2. changed reading the voxel spacing attrs

    Cristian Goina committed Jun 14, 2024
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  3. fixed attribute

    Cristian Goina committed Jun 14, 2024
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  4. more logs

    Cristian Goina committed Jun 14, 2024
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  5. NPE

    Cristian Goina committed Jun 14, 2024
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  6. removed some config entries

    Cristian Goina committed Jun 14, 2024
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Commits on Jun 15, 2024

  1. fixed step check

    Cristian Goina committed Jun 15, 2024
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  2. logging

    Cristian Goina committed Jun 15, 2024
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Commits on Jun 16, 2024

  1. fixed alignment and deform errors

    Cristian Goina committed Jun 16, 2024
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  2. removed debug messages

    Cristian Goina committed Jun 16, 2024
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  3. create a dataset if overwrite is set

    Cristian Goina committed Jun 16, 2024
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Commits on Jun 17, 2024

  1. option to write deformation vecor either in the worker or in the driver

    Cristian Goina committed Jun 17, 2024
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  2. flag to allow writing either directly in the worker or in the reduce … 

    …call
    Cristian Goina committed Jun 17, 2024
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  3. configured logging for global alignment

    Cristian Goina committed Jun 17, 2024
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  4. forgot logging args

    Cristian Goina committed Jun 17, 2024
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  5. Created plugin for dask worker log config

    Cristian Goina committed Jun 17, 2024
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  6. fixed configure logging

    Cristian Goina committed Jun 17, 2024
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  7. write log to stdout

    Cristian Goina committed Jun 17, 2024
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  8. fixed config

    Cristian Goina committed Jun 17, 2024
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  9. replaced printouts with logging for ransac

    Cristian Goina committed Jun 17, 2024
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Commits on Jun 18, 2024

  1. more prints replaced with logging

    Cristian Goina committed Jun 18, 2024
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  2. update register notebook

    Cristian Goina committed Jun 18, 2024
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  3. replaced more print statements with log statements

    Cristian Goina committed Jun 18, 2024
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Commits on Jun 20, 2024

  1. add logging support

    Cristian Goina committed Jun 20, 2024
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  2. arg for cluster max tasks

    Cristian Goina committed Jun 20, 2024
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Commits on Jun 21, 2024

  1. format logger.error

    Cristian Goina committed Jun 21, 2024
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Commits on Jun 25, 2024

  1. support for compression

    Cristian Goina committed Jun 25, 2024
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  2. Changed help text for compression

    Cristian Goina committed Jun 25, 2024
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Commits on Jun 26, 2024

  1. default to gzip - n5-spark does not support zstd

    Cristian Goina committed Jun 26, 2024
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  2. typo + formatting

    Cristian Goina committed Jun 26, 2024
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  3. logging

    Cristian Goina committed Jun 26, 2024
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Commits on Jun 27, 2024

  1. write inverse field in the worker

    Cristian Goina committed Jun 27, 2024
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  2. created a main function

    Cristian Goina committed Jun 27, 2024
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  3. close cluster client in a finally block

    Cristian Goina committed Jun 27, 2024
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  4. main script to compute the inverse

    Cristian Goina committed Jun 27, 2024
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  5. fixed compute inverse errors

    Cristian Goina committed Jun 27, 2024
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  6. remove aggregate writing

    Cristian Goina committed Jun 27, 2024
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  7. return futures with results

    Cristian Goina committed Jun 27, 2024
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  8. check that ITK_THREADS is not gt the number of cpus

    Cristian Goina committed Jun 27, 2024
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  9. Error fix (attempt)

    Cristian Goina committed Jun 27, 2024
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  10. plugin to set worker environment variables to restrict the number of … 

    …threads used by the numpy worker tasks
    Cristian Goina committed Jun 27, 2024
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Commits on Jun 28, 2024

  1. logging to figure out why the env plugin does not register

    Cristian Goina committed Jun 28, 2024
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  2. use register_worker_plugin

    Cristian Goina committed Jun 28, 2024
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  3. use register worker plugin

    Cristian Goina committed Jun 28, 2024
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  4. use str to set the env values

    Cristian Goina committed Jun 28, 2024
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  5. use async client

    Cristian Goina committed Jun 28, 2024
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  6. removed asyncio

    Cristian Goina committed Jun 28, 2024
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  7. unified the plugins for testing

    Cristian Goina committed Jun 28, 2024
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  8. comment out the environment setting

    Cristian Goina committed Jun 28, 2024
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  9. removed asyncio

    Cristian Goina committed Jun 28, 2024
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  10. write transformed blocks in the worker

    Cristian Goina committed Jun 28, 2024
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  11. check if itk_threads is also set

    Cristian Goina committed Jun 28, 2024
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  12. removed debug message

    Cristian Goina committed Jun 28, 2024
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  13. formatting log messages

    Cristian Goina committed Jun 28, 2024
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  14. option to set the cpus for global alignment

    Cristian Goina committed Jun 28, 2024
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  15. renamed configure_plugin to configure_bigstream

    Cristian Goina committed Jun 28, 2024
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Commits on Jun 29, 2024

  1. changed import order

    Cristian Goina committed Jun 29, 2024
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  2. rearraged imports

    Cristian Goina committed Jun 29, 2024
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  3. import package right before used

    Cristian Goina committed Jun 29, 2024
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  4. more changes to imports

    Cristian Goina committed Jun 29, 2024
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  5. use the methods from configure_bigstream

    Cristian Goina committed Jun 29, 2024
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  6. clear outputs

    Cristian Goina committed Jun 29, 2024
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  7. changed log message

    Cristian Goina committed Jun 29, 2024
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  8. formatting

    Cristian Goina committed Jun 29, 2024
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Commits on Jul 3, 2024

  1. fixed logging; made context parameter explicit for ransac so that it … 

    …doesn't get passed to cv2.estimateAffine
    Cristian Goina committed Jul 3, 2024
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Commits on Aug 5, 2024

  1. fixed logger call

    Cristian Goina committed Aug 5, 2024
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