Started to LOCI Bioformats opener for .tif files

Automatic reading of calibration from .tif files

spim_registration/timelapse/Snakefile

@@ -77,6 +77,7 @@ rule define_xml_tif:
         -Dchannels={channels} \
         -Dillumination={illumination} \
         -Dimage_file_pattern={image_file_pattern} \
+        -Dmanual_calibration_tif={manual_calibration_tif} \
         -Dpixel_distance_x={pixel_distance_x} \
         -Dpixel_distance_y={pixel_distance_y} \
         -Dpixel_distance_z={pixel_distance_z} \

spim_registration/timelapse/define_czi.bsh

@@ -174,10 +174,6 @@ IJ.run("Define Multi-View Dataset",
 	modify_calibration + 
 	"modify_rotation_axis " +
 	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 + " " +
 	"rotation_around=" + rotation_around + "");
 }
 catch ( e ) { 

spim_registration/timelapse/define_tif_zip.bsh

@@ -109,20 +109,46 @@ if (illumination.equalsIgnoreCase(""))
 		
 System.out.println( "Illuminations = " + illum_string );
 
+// Calibaration
 // Calibaration
 System.out.println("=========================================================");
 System.out.println("Calibration:");
-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" );
+manual_calibration_tif = System.getProperty( "manual_calibration_tif" );
+float czi_pixel_distance_x = Float.parseFloat( System.getProperty( "pixel_distance_x" ) );
+float czi_pixel_distance_y = Float.parseFloat( System.getProperty( "pixel_distance_y" ) );
+float czi_pixel_distance_z = Float.parseFloat( System.getProperty( "pixel_distance_z" ) );
+czi_pixel_unit = System.getProperty( "pixel_unit" );
+
+// builds string for calibration override
+if (manual_calibration_tif.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_tif.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 );
+}
 
-System.out.println( "pixel_distance_x = " + pixel_distance_x );
-System.out.println( "pixel_distance_y = " + pixel_distance_y );
-System.out.println( "pixel_distance_z = " + pixel_distance_z );
-System.out.println( "pixel_unit = " + pixel_unit );
+else
+{
+	System.out.println( "Manual calibration setting bad" );
+}
 
 
+System.out.println("=========================================================");
+System.out.println("Start plugin:");
+
 System.out.println("Define Multi-View Dataset , type_of_dataset=[" + type_of_dataset + "] " +
 	"xml_filename=[" + xml_filename + ".xml] " +
 	"multiple_timepoints=[" + multiple_timepoints + "] " +
@@ -135,16 +161,14 @@ System.out.println("Define Multi-View Dataset , type_of_dataset=[" + type_of_dat
 	channel_string +
 	illum_string +
 	"acquisition_angles_=" + acquisition_angles + " " +  
-	"calibration_type=[Same voxel-size for all views] calibration_definition=[User define voxel-size(s)]" + " " + 
-	"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 + "");
+	"calibration_type=[Same voxel-size for all views] " +
+	modify_calibration +
+	"imglib2_data_container=[" + imglib_container + "]" + 
+	manual_calibration_string +
+	"");
 
 // Executes Fiji plugin
-System.out.println("=========================================================");
-System.out.println("Start plugin:");
+
 try {
 IJ.run("Define Multi-View Dataset", 
 	"type_of_dataset=[" + type_of_dataset + "] " +
@@ -159,12 +183,11 @@ IJ.run("Define Multi-View Dataset",
 	channel_string +
 	illum_string +
 	"acquisition_angles_=" + angles + " " +  
-	"calibration_type=[Same voxel-size for all views] calibration_definition=[User define voxel-size(s)]" + " " + 
-	"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 + "");
+	"calibration_type=[Same voxel-size for all views] " +
+	modify_calibration + 
+	"imglib2_data_container=[" + imglib_container + "]" + 
+	manual_calibration_string +
+	"");
 }
 catch ( e ) { 
 

spim_registration/timelapse/single.yaml

@@ -52,7 +52,7 @@ common: {
   # ============================================================================
   ntimepoints: 72,               # number of timepoints of dataset
   angles: "0,72,144,216,288",   # angles
-  channels: "green",        # channels
+  channels: "green",        # channels, for tif numeric!
   illumination: "0",            # illuminations
   # ----------------------------------------------------------------------------
   # For .czi datasets
@@ -61,14 +61,10 @@ common: {
   # ----------------------------------------------------------------------------
   # For .tif datasets
   # file pattern of .tif files:
-  # for multi channel give spim_TL{tt}_Angle{a}_Channel{c}.tif
+  # for multi channel with one file per channel give spim_TL{tt}_Angle{a}_Channel{c}.tif
   # for padded zeros use tt 
-  # specify calibration
   image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif',
-  pixel_distance_x: '0.285901069641113',  # Manual calibration x
-  pixel_distance_y: '0.285901069641113',  # Manual calibration y
-  pixel_distance_z: '1.500000000000000',  # Manual calibration z
-  pixel_unit: "um",             # unit of manual calibration
+  multiple_channels: '"NO (one channel)"',         # '"YES (all channels in one file)"' or '"YES (one file per channel)"' or '"NO (one channel)"'
   # ============================================================================
   # Detection and registration
   #
@@ -187,7 +183,7 @@ common: {
   # ============================================================================
   
 define_xml_czi: {
-  manual_calibration_czi: "Yes", # calibration override: No or Yes
+  manual_calibration_czi: "No", # calibration override: No or Yes
   czi_pixel_distance_x: '0.285901069641113',  # Manual calibration x
   czi_pixel_distance_y: '0.285901069641113',  # Manual calibration y
   czi_pixel_distance_z: '1.500000000000000',  # Manual calibration z
@@ -198,10 +194,14 @@ define_xml_czi: {
   
 define_xml_tif: {
   # Settings for ImageJ Opener
-  type_of_dataset: '"Image Stacks (ImageJ Opener)"',
+  manual_calibration_tif: "No", # calibration override: No or Yes
+  pixel_distance_x: '0.285901069641113',  # Manual calibration x
+  pixel_distance_y: '0.285901069641113',  # Manual calibration y
+  pixel_distance_z: '1.500000000000000',  # Manual calibration z
+  pixel_unit: "um",             # unit of manual calibration
+  type_of_dataset: '"Image Stacks (LOCI Bioformats)"', # '"Image Stacks (ImageJ Opener)"' or '"Image Stacks (LOCI Bioformats)"'
   multiple_timepoints: '"YES (one file per time-point)"', # or NO (one time-point)
   multiple_angles: '"YES (one file per angle)"',          # or NO (one angle)
-  multiple_channels: '"NO (one channel)"',                # or "\"NO (one channel)\""
   multiple_illumination_directions: '"NO (one illumination direction)"', # or YES (one file per illumination direction)
   imglib_container: '"ArrayImg (faster)"',        # '"ArrayImg (faster)"'
   bsh_file: "define_tif_zip.bsh"