import os, glob, sys

#where are we
if "datadir" not in config.keys():
   JOBDIR=os.path.abspath(os.path.curdir)
else:
   if os.path.isdir(config['datadir']):
      JOBDIR=config['datadir']
   else:
      print("given data dir does not exist {data}".format(data=config['datadir']))
      sys.exit(1)

if JOBDIR[-1] != "/":
   JOBDIR+="/"
   
datasets = glob.glob('*00.h5') 

#data specific config file
configfile: "tomancak.json"

def produce_string(_fstring, *args, **kwargs):
   contents = dict()
   for item in args:
      if type(item) == type(kwargs):
         contents.update(item)
         
   contents.update(kwargs)
   return _fstring.format(**contents)

rule done:
    input: [ ds+"-deconvolved" for ds in datasets ]
    
rule registration:
    input: "{xml_base}-{file_id,\d+}-00.h5"
    output: "{xml_base}-{file_id,\d+}-00.h5_registered", #convenience files
            "{xml_base}.job_{file_id,\d+}.xml"
    log: "{xml_base}-{file_id,\d+}-registration.log"
    run:
        cmd_string = produce_string(
           """{fiji-prefix} {fiji-app} \
-Dparallel_timepoints={file_id_w} \
-Dimage_file_directory={jdir} \
-Dxml_filename={input_xml} \
-Dprocess_timepoint={timepoint} \
-Dprocess_channel={channel} \
-Dprocess_illumination={illuminations} \
-Dprocess_angle={angle} \
-Dprocessing_channel={proc-ch} \
-Dlabel_interest_points={label_interest_points} \
-Dtype_of_registration={type_of_registration} \
-Dtype_of_detection={type_of_detection} \
-Dsubpixel_localization={subpixel_localization} \
-Dimglib_container={imglib_container} \
-Dradius_1={radius_1} \
-Dradius_2={radius_2} \
-Dthreshold={threshold} \
-Dinitial_sigma={initial_sigma} \
-Dthreshold_gaussian={threshold_gaussian} \
-Dregistration_algorithm={algorithm} \
-Dinterest_points_channel_0={interest_points_channel_0} \
-Dinterest_points_channel_1={interest_points_channel_1} \
-Dfix_tiles={fix_tiles} \
-Dmap_back_tiles={map_back_tiles} \
-Dtransformation_model={transformation_model} \
-Dmodel_to_regularize_with={model_to_regularize_with} \
-Dlambda={lambda} \
-Dallowed_error_for_ransac={allowed_error_for_ransac} \
-Ddetection_min_max={detection_min_max} \
-- --no-splash {bsh_file}""",
           config["common"], 
           config["registration"],
           file_id_w="{wildcards.file_id}",
           jdir=JOBDIR,
           input_xml="{wildcards.xml_base}")
        cmd_string += "> {log} 2>&1 && touch {output}"
        shell(cmd_string)
        #shell("touch {output}")

rule xml_merge:
    input: [ item+"_registered" for item in datasets ]
    output: "{xml_base}_merge.xml"
    log: "{xml_base}_merge.log"
    run:
        cmd_string = produce_string("{fiji-prefix} {fiji-app} -Dimage_file_directory={jdir} -Dmerged_xml={merged_xml} -- --no-splash {bsh_file} > {log} 2>&1",
                                    config["common"],
                                    config["xml_merge"],
                                    log="{log}",
                                    jdir=JOBDIR)
        shell(cmd_string)

rule external_trafo:
    input: rules.xml_merge.output
    output: rules.xml_merge.output[0] + "_external_trafo"
    log: "external_trafo.log"
#    message: "etrafo {input} -> {output}"
    run:
        cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dmerged_xml={merged_xml} \
-Dtransform_angle={angle} \
-Dtransform_channel={channel} \
-Dtransform_illumination={illumination} \
-Dtransform_timepoint={timepoint} \
-Dtransformation={transformation} \
-Dapply_transformation={apply_transformation} \
-Ddefine_mode_transform={define_mode_transform} \
-Dmatrix_transform={matrix_transform} \
-- --no-splash {bsh_file}""",
                                    config["common"], 
                                    config["external_transform"],
                                    jdir=JOBDIR)
        cmd_string += "> {log} 2>&1 && touch {output}"
        shell(cmd_string)

rule deconvolution:
    input: rules.external_trafo.output, "{xml_base}-{file_id,\d+}-00.h5"
    output: "{xml_base}-{file_id,\d+}-00.h5-deconvolved"
    log: "{xml_base}-{file_id,\d+}-00.h5-deconvolution.log"
    run:
        cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Ddeco_output_file_directory={jdir} \
-Dmerged_xml={merged_xml} \
-Dparallel_timepoints={file_id_w} \
-Dprocess_timepoint={process_timepoint} \
-Dprocess_channel={process_channel} \
-Dprocess_illumination={process_illumination} \
-Dprocess_angle={process_angle} \
-Dminimal_x_deco={minimal_x} \
-Dminimal_y_deco={minimal_y} \
-Dminimal_z_deco={minimal_z} \
-Dmaximal_x_deco={maximal_x} \
-Dmaximal_y_deco={maximal_y} \
-Dmaximal_z_deco={maximal_z} \
-Dimglib2_container_deco={imglib2_container} \
-Dtype_of_iteration={type_of_iteration} \
-Dosem_acceleration={osem_acceleration} \
-DTikhonov_parameter={Tikhonov_parameter} \
-Dcompute={compute} \
-Dpsf_estimation={psf_estimation} \
-Ddirectory_cuda={directory_cuda} \
-Ddetections_to_extract_psf_for_channel_0={detections_to_extract_psf_for_channel_0} \
-Ddetections_to_extract_psf_for_channel_1={detections_to_extract_psf_for_channel_1} \
-Dpsf_size_x={psf_size_x} \
-Dpsf_size_y={psf_size_y} \
-Dpsf_size_z={psf_size_z} \
-Diterations={iterations} \
-- --no-splash {bsh_file}""",
                                    config["common"], 
                                    config["deconvolution"],
                                    file_id_w="{wildcards.file_id}",
                                    jdir=JOBDIR)
        cmd_string += "> {log} 2>&1 && touch {output}"
        shell(cmd_string)
  
rule clean:
    shell : "rm -rf *registered"