Simplyfied output resaving

spim_registration/timelapse/Snakefile

@@ -65,7 +65,7 @@ rule define_xml_czi:
         
 # defining xml for tif dataset
 rule define_xml_tif:
-    input: glob.glob(re.sub("{{.}}","*",config["common"]['image_file_pattern'])) #replaces all occurrences of {{a}} (a can be any character) by * to use the string for globbing
+    input: glob.glob(re.sub("{{.}}","*", config["common"]['image_file_pattern'])) #replaces all occurrences of {{a}} (a can be any character) by * to use the string for globbing
     output: temp(config["common"]["first_xml_filename"] + ".xml")
     log: "logs/a2_define_xml_tif.log"
     run:
@@ -164,7 +164,7 @@ rule resave_hdf5:
         shell(part_string) 
        	       	
 rule registration:
-    input:  "{xml_base}-{file_id}-00.h5", expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"])
+    input:  rules.resave_hdf5.output, expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]) # "{xml_base}-{file_id}-00.h5"
     output: temp("{xml_base}.job_{file_id,\d+}.xml") #, "{xml_base}-{file_id,\d+}-00.h5_registered", 
     log: "logs/c_{xml_base}-{file_id}-registration.log"
     run:
@@ -414,7 +414,7 @@ rule deconvolution:
         shell(cmd_string)
 
 rule define_output:
-    input: [ item + "_" + config["common"]["fusion_switch"] for item in datasets ], glob.glob('TP*')
+    input: glob.glob('TP*'), [ item + "_" + config["common"]["fusion_switch"] for item in datasets ]
     output: temp(config["common"]["output_xml"].strip('\"') + ".xml")
     log: "logs/f1_define_output.log"
     run:
@@ -424,6 +424,7 @@ rule define_output:
         -Dtimepoints={output_timepoints} \
         -Dchannels={output_channels} \
         -Dimage_file_pattern={output_image_file_pattern} \
+        -Dmanual_calibration_output={manual_calibration_output} \
         -Dpixel_distance_x={output_pixel_distance_x} \
         -Dpixel_distance_y={output_pixel_distance_y} \
         -Dpixel_distance_z={output_pixel_distance_z} \
@@ -465,7 +466,7 @@ rule hdf5_xml_output:
                 -Dtimepoints_per_partition={timepoints_per_partition} \
                 -Dsetups_per_partition={setups_per_partition} \
                 -Drun_only_job_number=0 \
-                -Doutput_data_type={output_data_type} \
+                -Dfusion_switch={fusion_switch} \
                 -Dconvert_32bit={convert_32bit}\
                 -- --no-splash {path_bsh}""", 
            config["common"],
@@ -496,7 +497,7 @@ rule resave_hdf5_output:
         -Dtimepoints_per_partition={timepoints_per_partition} \
         -Dsetups_per_partition={setups_per_partition} \
         -Drun_only_job_number={job_number} \
-        -Doutput_data_type={output_data_type} \
+        -Dfusion_switch={fusion_switch} \
         -Dconvert_32bit={convert_32bit}\
         -- --no-splash {path_bsh}""", 
            config["common"],

spim_registration/timelapse/config.yaml

@@ -40,8 +40,15 @@ common: {
   # xml file names without .xml suffix
   # ============================================================================
   first_xml_filename: 'Dpse_Dip3_VK33',       # Name of the xml file for the .czi or .tif files
+  #
+  ########### simplyfy! ########################################################
   hdf5_xml_filename: '"hdf5_Dpse_Dip3_VK33"', # Name of .xml file for the hdf5 data after resave_hdf5
   merged_xml: 'hdf5_Dpse_Dip3_VK33_merge',    # Name of .xml file after merge
+  #
+  # .xml file names
+  output_xml: '"fused_Dpse_Dip3_VK33"',
+  output_hdf5_xml: '"hdf5_fused_Dpse_Dip3_VK33"',
+  #
   # ============================================================================
   # Describe the dataset
   #
@@ -153,31 +160,25 @@ common: {
   #          Image type (16Bit from content-based fusion, 32Bit from deconvolution)
   # ============================================================================
   # Number of timepoints
-  output_timepoints: '0-71',   # Timepoints format: '1-2'
+  output_timepoints: '0-1',   # Timepoints format: '1-2'
   #
   # Naming pattern:
   # Single Channel: TP{{t}}_Chgreen_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
   # Dual Channel: TP{{t}}_Ch{{0}}_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
-  output_image_file_pattern: '"TP{{t}}_Chgreen_Ill0_Ang0,72,144,216,288.tif"',
+  output_image_file_pattern: '"TP{{t}}_Ch0_Ill0_Ang1,2,3,4,5.tif"',
   #
   # channel setting:
   # Single channel: '"NO (one channel)"'
   # Dual channel: '"YES (one file per channel)"'
   output_multiple_channels: '"NO (one channel)"',
   output_channels: "green",
-  #
-  # .xml file names
-  output_xml: '"fused_Dpse_Dip3_VK33"',
-  output_hdf5_xml: '"hdf5_fused_Dpse_Dip3_VK33"',
-  #
+  # Calibration
+  manual_calibration_output: "Yes", # calibration override: No or Yes
   # pixel size of output: take downsampling into account!
   output_pixel_distance_x: 0.285901069641113, 
   output_pixel_distance_y: 0.285901069641113,
   output_pixel_distance_z: 0.285901069641113,
-  output_pixel_unit: 'um',
-  #
-  # File type
-  output_data_type: "16Bit" # "32Bit" or "16Bit"
+  output_pixel_unit: 'um'
   }
   # ============================================================================
   # Advanced settings
@@ -341,12 +342,13 @@ hdf5_output: {
   # subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}} }}"',
   # chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}} }}"',
   # Standard settings for hdf5_output
-  output_type_of_dataset: '"Image Stacks (ImageJ Opener)"',
+  output_type_of_dataset: '"Image Stacks (LOCI Bioformats)"', # '"Image Stacks (ImageJ Opener)"' or '"Image Stacks (LOCI Bioformats)"'
   output_multiple_timepoints: '"YES (one file per time-point)"',
   output_multiple_angles: '"NO (one angle)"',
   output_illumination_directions: '"NO (one illumination direction)"',
   output_imglib_container: '"ArrayImg (faster)"',
   num_cores_hdf5_xml_output: 2,
+  num_cores_resave_hdf5_output: 2,
   bsh_file_define: "define_output.bsh", # .bsh script for defining the dataset
   bsh_file_hdf5: "export_output.bsh"    # .bsh script for resaving into hdf5
   }

spim_registration/timelapse/define_output.bsh

@@ -83,6 +83,42 @@ else {
 
 }
 
+// Calibaration
+System.out.println("=========================================================");
+System.out.println("Calibration:");
+manual_calibration_output = System.getProperty( "manual_calibration_output" );
+float pixel_distance_x = Float.parseFloat( System.getProperty( "pixel_distance_x" ) );
+float pixel_distance_y = Float.parseFloat( System.getProperty( "pixel_distance_y" ) );
+float pixel_distance_z = Float.parseFloat( System.getProperty( "pixel_distance_z" ) );
+pixel_unit = System.getProperty( "pixel_unit" );
+
+// builds string for calibration override
+if (manual_calibration_output.equalsIgnoreCase( "No" ) )
+{
+	modify_calibration = "calibration_definition=[Load voxel-size(s) from file(s)] ";
+	manual_calibration_string = "";
+	System.out.println( modify_calibration );
+}
+
+else if (manual_calibration_output.equalsIgnoreCase( "Yes" ) )
+{
+	
+	modify_calibration = "calibration_definition=[User define voxel-size(s)] ";
+	manual_calibration_string = " pixel_distance_x=" + pixel_distance_x + " " +
+				    "pixel_distance_y=" + pixel_distance_y + " " +
+				    "pixel_distance_z=" + pixel_distance_z + " " +
+				    "pixel_unit=" + pixel_unit + " ";
+	System.out.println( "Calibration set to manual" );
+	System.out.println( modify_calibration );
+	System.out.println( "manual_calibration_string:" + manual_calibration_string );
+}
+
+else
+{
+	System.out.println( "Manual calibration setting bad" );
+}
+
+
 System.out.println( "channels = " + channels );
 
 System.out.println("Define Multi-View Dataset , type_of_dataset=[" + type_of_dataset + "] " +
@@ -95,12 +131,11 @@ System.out.println("Define Multi-View Dataset , type_of_dataset=[" + type_of_dat
 	"image_file_pattern=" + image_file_pattern + " " + 
 	"timepoints_=" + timepoints + " " +
 	channels +
-	"calibration_type=[Same voxel-size for all views] calibration_definition=[User define voxel-size(s)]" + " " + 
+	"calibration_type=[Same voxel-size for all views] " +
+	modify_calibration + 
 	"imglib2_data_container=[" + imglib_container + "] " + 
-	"pixel_distance_x=" + pixel_distance_x + " " + 
-	"pixel_distance_y=" + pixel_distance_y + " " + 
-	"pixel_distance_z=" + pixel_distance_z + " " +
-	"pixel_unit=" + pixel_unit + "");
+	manual_calibration_string +
+	"");
 
 // Executes Fiji plugin
 System.out.println("=========================================================");
@@ -117,12 +152,11 @@ IJ.run("Define Multi-View Dataset",
 	"image_file_pattern=" + image_file_pattern + " " + 
 	"timepoints_=" + timepoints + " " +
 	channels +
-	"calibration_type=[Same voxel-size for all views] calibration_definition=[User define voxel-size(s)]" + " " + 
+	"calibration_type=[Same voxel-size for all views] " +
+	modify_calibration + 
 	"imglib2_data_container=[" + imglib_container + "] " + 
-	"pixel_distance_x=" + pixel_distance_x + " " + 
-	"pixel_distance_y=" + pixel_distance_y + " " + 
-	"pixel_distance_z=" + pixel_distance_z + " " +
-	"pixel_unit=" + pixel_unit + "");
+	manual_calibration_string +
+	"");
 }
 catch ( e ) { 
 

spim_registration/timelapse/define_tif_zip.bsh

@@ -109,7 +109,6 @@ if (illumination.equalsIgnoreCase(""))
 		
 System.out.println( "Illuminations = " + illum_string );
 
-// Calibaration
 // Calibaration
 System.out.println("=========================================================");
 System.out.println("Calibration:");

spim_registration/timelapse/export_output.bsh

@@ -54,22 +54,21 @@ System.out.println( "setups_per_partition=" + setups_per_partition );
 System.out.println( "run_only_job_number=" + run_only_job_number );
 
 // Add a switch for choosing between 16 or 32 bit
-output_data_type = System.getProperty( "output_data_type" );
-System.out.println( "Output Datatype = " + output_data_type );
+fusion_switch = System.getProperty( "fusion_switch" );
+System.out.println( "Output Datatype = " + fusion_switch );
 
 convert_32bit = System.getProperty( "convert_32bit" );
 
-if ( output_data_type.equalsIgnoreCase( "32Bit" ) )
+if ( fusion_switch.equalsIgnoreCase( "deconvolution" ) )
 	{
 		data_string = "convert_32bit=" + convert_32bit;
+		System.out.println( "Data string = " + data_string );
 	}
-else if ( output_data_type.equalsIgnoreCase( "16Bit" ) )
+else if ( fusion_switch.equalsIgnoreCase( "fusion" ) )
 	{
 		data_string = "";
 	}
 
-System.out.println( "Data string = " + data_string );
-
 // Activate cluster processing
 System.out.println("=========================================================");
 System.out.println("Cluster setting:");