Started to add define xml

spim_registration/timelapse/Snakefile

@@ -6,7 +6,7 @@ if JOBDIR[-1] != "/":
    JOBDIR+="/"
 
 #data specific config file, expected to be inside JOBDIR
-configfile: "tomancak.json"
+configfile: "tomancak_czi.json"
    
 datasets = glob.glob('*00.h5')
 
@@ -32,6 +32,38 @@ def produce_string(_fstring, *args, **kwargs):
 rule done:
     input: [ ds+"_deconvolved" for ds in datasets ]
 
+# add part for defining xml file on czi dataset
+rule define_xml:
+	input: "{czi_base}.czi"
+	output: "{xml_name}.xml"
+	threads: 1
+	message: "Execute define xml with {threads} threads on the following files {input}"
+	log: "define_xml.log"
+	run: cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
+	-Dimage_file_directory={jdir}\
+	-Dfirst_czi={first_czi} \
+	-Dangle_1={angle_1} \
+	-Dangle_2={angle_2} \
+	-Dangle_3={angle_3} \
+	-Dangle_4={angle_4} \
+	-Dangle_5={angle_5} \
+	-Dchannel_1={channel_1} \
+	-Dchannel_2={channel_2} \
+	-Dillumination_1={illumination_1} \
+	-Drotation_around={rotation_around} \
+	-Dpixel_distance_x={pixel_distance_x} \
+	-Dpixel_distance_y={pixel_distance_y} \
+	-Dpixel_distance_z={pixel_distance_z} \
+	-Dpixel_unit={pixel_unit} \
+	-Dfirst_xml_filename={first_xml_filename} \
+	-- --no-splash {bsh_file}""",
+	config["common"],
+	config["define_xml_czi"],
+	jdir=JOBDIR,
+	output="{output}")
+	
+	shell(cmd_string)
+	
 rule registration:
     input: "{xml_base}-{file_id}-00.h5"
     output: "{xml_base}-{file_id,\d+}-00.h5_registered", #"{xml_base}.job_{file_id,\d+}.xml"

spim_registration/timelapse/tomancak_czi.json

+{
+    "common" :
+    {
+	"fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher-sandbox/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
+	"fiji-prefix" : "/sw/bin/xvfb-run -a",
+	"directory_cuda" : "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
+	"merged_xml" : "hdf5_test_unicore_merge"
+    },
+    
+    "define_xml_czi" :
+    {
+    	    "pixel_distance_x" : "0.2875535786151886" 	# Manual calibration x
+    	    "pixel_distance_y" : "0.2875535786151886" 	# Manual calibration y
+    	    "pixel_distance_z" : "1.50000" 	# Manual calibration z
+    	    "pixel_unit" : "um"			# unit of manual calibration	    
+    	    "first_czi" : "2015-02-21_LZ1_Stock68_3.czi"
+    	    "angle_1" : "0"
+    	    "angle_2" : "72"
+    	    "angle_3" :"144"
+    	    "angle_4" :"216"
+    	    "angle_5" : "288"
+    	    "illumination_1" : "0"
+    	    "bsh_file" : "define_czi.bsh"    
+    },
+    
+    "registration" :
+    {
+	"timepoint" : "\"Single Timepoint (Select from List)\"",
+	"illuminations" : "\"All illuminations\"",
+	"angle" : "\"All angles\"",
+	"channel" : "\"All channels\"",
+	"proc-ch" : "\"channel 1\"",
+	"algorithm" : "\"Fast 3d geometric hashing (rotation invariant)\"",
+	"label_interest_points" : "\"beads\"",
+	"type_of_registration" : "\"Register timepoints individually\"",
+	"type_of_registration_timelapse" : "\"Match against one reference timepoint (no global optimization)\"",
+	"type_of_detection" : "\"Difference-of-Mean (Integral image based)\"" ,
+	"subpixel_localization" : "\"3-dimensional quadratic fit\"",
+	"imglib_container" : "\"ArrayImg (faster)\"",
+	"radius_1" : "2",
+	"radius_2" : "3",
+	"threshold" : "0.005",
+	"interest_points_channel_0" : "\"[DO NOT register this channel]\"" ,
+	"interest_points_channel_1" : "\"beads\"",
+	"fix_tiles" : "\"Fix first tile\""	,
+	"map_back_tiles" : "\"Map back to first tile using rigid model\"",
+	"transformation_model" : "Affine",
+	"model_to_regularize_with" : "Rigid",
+	"lambda" : "0.10" ,
+	"allowed_error_for_ransac" : "5",
+	"detection_min_max" : "find_maxima",
+	"initial_sigma" : "1.8",
+	"threshold_gaussian" : "0.0080",
+	"bsh_file" : "registration.bsh"
+    },
+ 
+    "xml_merge" :
+    {
+	"bsh_file" : "xml_merge.bsh"
+    },
+
+    "external_transform" :
+    {
+	"bsh_file" : "transform.bsh",
+	"angle" : "\"All angles\"",
+	"channel" : "\"All channels\"",
+	"illumination" : "\"All illuminations\"",
+	"timepoint" : "\"All Timepoints\"",
+	"transformation" : "\"Rigid\"",
+	"apply_transformation" : "\"Current view transformations (appends to current transforms)\"",
+	"define_mode_transform" : "\"Matrix\"",
+	"matrix_transform" : "\"0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0\""
+    },
+
+    "deconvolution" :
+    {
+
+	"bsh_file" : "deconvolution_GPU.bsh",
+	"process_timepoint" : "\"Single Timepoint (Select from List)\"",
+	"process_channel" : "\"All channels\"",
+	"process_illumination" : "\"All illuminations\"",
+	"process_angle" : "\"All angles\"",
+	"minimal_x" : "76",
+	"minimal_y" : "4",
+	"minimal_z" : "-192",
+	"maximal_x" : "488",
+	"maximal_y" : "956",
+	"maximal_z" : "214",
+	"imglib2_container" : "\"ArrayImg \"",
+	"type_of_iteration" : "\"Efficient Bayesian - Optimization I (fast, precise)\"",
+	"osem_acceleration" : "\"1 (balanced)\"",
+	"Tikhonov_parameter" : "0.0006",
+	"compute" : "\"in 512x512x512 blocks\"",
+	"compute_on" : "\"GPU (Nvidia CUDA via JNA)\"",
+	"psf_estimation" : "\"Extract from beads\"",
+	"iterations" : "5",
+	"detections_to_extract_psf_for_channel_0" : "\"beads\"",
+	"detections_to_extract_psf_for_channel_1" : "\"beads\"",
+	"psf_size_x" : "19",
+	"psf_size_y" : "19",
+	"psf_size_z" : "25"
+    }
+    
+}