From acdaec1a1f7f6a5f3322c0ee7229cc98abe6671a Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Tue, 14 Jul 2015 18:57:50 +0200
Subject: [PATCH] Calibration for czi is read out automatically added tempfiles
---
spim_registration/timelapse/Snakefile | 30 +++++------
spim_registration/timelapse/define_czi.bsh | 63 ++++++++++++++--------
2 files changed, 56 insertions(+), 37 deletions(-)
mode change 100644 => 100755 spim_registration/timelapse/define_czi.bsh
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 39cf6ae..59f4704 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -26,11 +26,8 @@ xml_merge_in = produce_xml_merge_job_files(datasets)
rule done:
input: [ ds + "_output_hdf5" for ds in datasets ]
-localrules: define_xml_czi, define_xml_tif, hdf5_xml, xml_merge, timelapse,
- duplicate_transformations, external_transform, define_output,
- hdf5_xml_output
-
-
+localrules: define_xml_tif, xml_merge, timelapse,
+ duplicate_transformations, external_transform, define_output
rule resave_prepared:
input: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"] ], suffix=["xml","h5"])
@@ -47,10 +44,11 @@ rule define_xml_czi:
-Dangles={angles} \
-Dchannels={channels} \
-Dillumination={illumination} \
- -Dpixel_distance_x={pixel_distance_x} \
- -Dpixel_distance_y={pixel_distance_y} \
- -Dpixel_distance_z={pixel_distance_z} \
- -Dpixel_unit={pixel_unit} \
+ -Dmanual_calibration_czi={manual_calibration_czi} \
+ -Dczi_pixel_distance_x={czi_pixel_distance_x} \
+ -Dczi_pixel_distance_y={czi_pixel_distance_y} \
+ -Dczi_pixel_distance_z={czi_pixel_distance_z} \
+ -Dczi_pixel_unit={czi_pixel_unit} \
-Dfirst_xml_filename={first_xml_filename} \
-Drotation_around={rotation_around} \
-- --no-splash {path_bsh}""",
@@ -66,7 +64,7 @@ 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
- output: config["common"]["first_xml_filename"] + ".xml"
+ output: temp(config["common"]["first_xml_filename"] + ".xml")
log: "logs/a2_define_xml_tif.log"
run:
cmd_string = produce_string(
@@ -105,7 +103,7 @@ ruleorder: define_xml_czi > define_xml_tif
rule hdf5_xml:
input: config["common"]["first_xml_filename"] + ".xml"
output: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]),
- [ item+"_xml" for item in datasets ]
+ temp([ item+"_xml" for item in datasets ])
log: "logs/b1_hdf5_xml.log"
run:
part_string = produce_string(
@@ -236,7 +234,7 @@ rule xml_merge:
rule timelapse:
input: rules.xml_merge.output
- output: rules.xml_merge.output[0] + "_timelapse"
+ output: temp(rules.xml_merge.output[0] + "_timelapse")
log: "logs/d2_{xml_base}_timelapse.log"
run:
cmd_string = produce_string(
@@ -269,7 +267,7 @@ rule timelapse:
rule duplicate_transformations:
input: rules.timelapse.output, merged_xml="{xml_base}_merge.xml"
- output: rules.timelapse.output[0] + "_duplicate"
+ output: temp(rules.timelapse.output[0] + "_duplicate")
log: "logs/d3_{xml_base}_duplicate_transformations.log"
run:
cmd_string = produce_string(
@@ -296,7 +294,7 @@ rule duplicate_transformations:
rule fusion:
input: [ str("{xml_base}_merge.xml_" + config["common"]["transformation_switch"] ) ], "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml" # rules.timelapse.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml"
- output: "{xml_base}-{file_id,\d+}-00.h5_fusion"
+ output: temp("{xml_base}-{file_id,\d+}-00.h5_fusion")
log: "logs/e1_{xml_base}-{file_id,\d+}-00-fusion.log"
run:
cmd_string = produce_string(
@@ -339,7 +337,7 @@ rule fusion:
rule external_transform:
input: rules.timelapse.output, merged_xml="{xml_base}_merge.xml"
- output: rules.timelapse.output[0] + "_external_trafo"
+ output: temp(rules.timelapse.output[0] + "_external_trafo")
log: "logs/e2_external_transform.log"
run:
cmd_string = produce_string(
@@ -367,7 +365,7 @@ rule external_transform:
rule deconvolution:
input: [ str("{xml_base}_merge.xml_" + config["common"]["transformation_switch"] ) ], "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml" # rules.timelapse.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml" # rules.external_transform.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml"
- output: "{xml_base}-{file_id,\d+}-00.h5_deconvolution"
+ output: temp("{xml_base}-{file_id,\d+}-00.h5_deconvolution")
log: "logs/e2_{xml_base}-{file_id,\d+}-00-deconvolution.log"
run:
cmd_string = produce_string(
diff --git a/spim_registration/timelapse/define_czi.bsh b/spim_registration/timelapse/define_czi.bsh
old mode 100644
new mode 100755
index aa6b052..da8ea05
--- a/spim_registration/timelapse/define_czi.bsh
+++ b/spim_registration/timelapse/define_czi.bsh
@@ -9,8 +9,8 @@ import java.io.FilenameFilter;
runtime = Runtime.getRuntime();
System.out.println(runtime.availableProcessors() + " cores available for multi-threading");
-//Prefs.setThreads(2); // defines the number of threads allowed
-//print("Threads: "+Prefs.getThreads()); // prints thread setting in output
+Prefs.setThreads(1); // defines the number of threads allowed
+print("Threads: "+Prefs.getThreads()); // prints thread setting in output
System.out.println("Start loading parameters");
@@ -114,15 +114,37 @@ System.out.println( "rotation_around = " + rotation_around );
// 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_czi = System.getProperty( "manual_calibration_czi" );
+float czi_pixel_distance_x = Float.parseFloat( System.getProperty( "czi_pixel_distance_x" ) );
+float czi_pixel_distance_y = Float.parseFloat( System.getProperty( "czi_pixel_distance_y" ) );
+float czi_pixel_distance_z = Float.parseFloat( System.getProperty( "czi_pixel_distance_z" ) );
+czi_pixel_unit = System.getProperty( "czi_pixel_unit" );
+
+// builds string for calibration override
+if (manual_calibration_czi.equalsIgnoreCase( "No" ) )
+{
+ modify_calibration = "";
+ manual_calibration_string = "";
+ System.out.println( "Calibration set to automatic" );
+}
-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 if (manual_calibration_czi.equalsIgnoreCase( "Yes" ) )
+{
+
+ modify_calibration = "modify_calibration ";
+ manual_calibration_string = "pixel_distance_x=" + czi_pixel_distance_x + " " +
+ "pixel_distance_y=" + czi_pixel_distance_y + " " +
+ "pixel_distance_z=" + czi_pixel_distance_z + " " +
+ "pixel_unit=" + czi_pixel_unit + " ";
+ System.out.println( "Calibration set to manual" );
+ System.out.println( "modify_calibration:" + modify_calibration );
+ System.out.println( "manual_calibration_string:" + manual_calibration_string );
+}
+
+else
+{
+ System.out.println( "Manual calibration setting bad" );
+}
// Executes Fiji plugin
System.out.println("=========================================================");
@@ -134,13 +156,11 @@ System.out.println("Define Multi-View Dataset type_of_dataset=[Zeiss Lightsheet
angle_string +
channel_string +
illum_string +
- "modify_calibration " +
+ modify_calibration +
"modify_rotation_axis " +
- "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 + "");
+ manual_calibration_string +
+ "rotation_around=" + rotation_around +
+ "");
try {
IJ.run("Define Multi-View Dataset",
@@ -151,12 +171,13 @@ IJ.run("Define Multi-View Dataset",
angle_string +
channel_string +
illum_string +
- "modify_calibration " +
+ modify_calibration +
"modify_rotation_axis " +
- "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 +
+ //"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 ) {
--
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