From 3debfb9dcc0e5e197c8921ed50323e1c40446d9d Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Wed, 15 Jul 2015 18:14:48 +0200
Subject: [PATCH] Started to LOCI Bioformats opener for .tif files
Automatic reading of calibration from .tif files
---
spim_registration/timelapse/Snakefile | 1 +
spim_registration/timelapse/define_czi.bsh | 4 --
.../timelapse/define_tif_zip.bsh | 67 +++++++++++++------
spim_registration/timelapse/single.yaml | 20 +++---
4 files changed, 56 insertions(+), 36 deletions(-)
mode change 100644 => 100755 spim_registration/timelapse/define_tif_zip.bsh
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 11a8765..6351d4a 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/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} \
diff --git a/spim_registration/timelapse/define_czi.bsh b/spim_registration/timelapse/define_czi.bsh
index da8ea05..532b0d6 100755
--- a/spim_registration/timelapse/define_czi.bsh
+++ b/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 ) {
diff --git a/spim_registration/timelapse/define_tif_zip.bsh b/spim_registration/timelapse/define_tif_zip.bsh
old mode 100644
new mode 100755
index a5f4015..8108d62
--- a/spim_registration/timelapse/define_tif_zip.bsh
+++ b/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 ) {
diff --git a/spim_registration/timelapse/single.yaml b/spim_registration/timelapse/single.yaml
index d6eef5f..2275fa9 100755
--- a/spim_registration/timelapse/single.yaml
+++ b/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"
--
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