redlionfish.py

"""
Copyright 2021 Rosalind Franklin Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
"""

#To be run from the command line
#It needs to be a seperate file otherwise the imports will fail

__version__ = "0.9"

# Ability to run from command line providing tiff (or other) filenames
def main():
    import argparse
    import os
    import sys

    #Argument to showInfo overrides the required arguments
    #The way to achieve this is to create an Action.
    #https://docs.python.org/dev/library/argparse.html#action
    class showInfoAction(argparse.Action):
        # def __init__(self, option_strings, dest, nargs=None, **kwargs):
        #     if nargs is not None:
        #         raise ValueError("nargs not allowed")
        #     super().__init__(option_strings, dest, **kwargs)
        def __call__(self, parser, namespace, values, option_string=None):
            import RedLionfishDeconv.RLDeconv3DReiknaOCL as rlfocl
            if rlfocl.isReiknaAvailable:
                print ("Reikna (OpenCL) is available.")
                #Get GPU info
                rlfocl.printGPUInfo()
            else:
                print("Reikna (OpenCL) is NOT available.")
            parser.exit()

    parser = argparse.ArgumentParser(description="Richardson-Lucy deconvolution of 3D data.")
    argp_group1 = parser.add_argument_group('files', 'RL from files')
    argp_group1.add_argument("data3Dpath", help="Input 3d data file, tiff format")
    argp_group1.add_argument("psf3Dpath" , help="Input 3d psf/otf file, tiff format")
    argp_group1.add_argument("iterations", type=int, default=10, help="Number of iterations")
    argp_group1.add_argument("--outpath" , "-o", help="output filanme")
    argp_group1.add_argument("--method" , help = "force gpu or cpu method. (not implemented yet, automatic, trying gpu first).")

    argp_group2 = parser.add_argument_group('info', 'Various information')
    argp_group2.add_argument("--version", "-v", action="version", version=__version__ , help = "Show version information")
    argp_group2.add_argument("--showinfo", action=showInfoAction , nargs=0, help = "Show GPU information. Useful before high-processing power testing.")

    args= parser.parse_args()

    data3Dpath = args.data3Dpath
    #check files data3Dpath and psf3Dpath exist
    if not os.path.exists(data3Dpath) :
        print(f"File {data3Dpath} could not be found. Exiting.")
        sys.exit()

    psf3Dpath = args.psf3Dpath
    if not os.path.exists(psf3Dpath) :
        print(f"File {psf3Dpath} could not be found. Exiting.")
        sys.exit()

    iterations = args.iterations
    if iterations <=0:
        print(f"Invalid number of iterations {iterations}")
        sys.exit
    
    #setup the filename.
    # if not provided use the data filname with added _it<iterations>.tiff
    outpath = args.outpath
    if outpath is None:
        pathhead, pathtail = os.path.split(args.data3Dpath)
        pathname , ext = os.path.splitext(pathtail)
        outpath = pathname + "_it" + str(iterations) + ".tiff"

    import RedLionfishDeconv as rl
    _ = rl.doRLDeconvolutionFromFiles(data3Dpath, psf3Dpath, iterations, savepath=outpath)

if __name__ == "__main__":
    # Run if called from the command line
    main()