From 28c9a49f86d5f669812d2993d73a871b6f799009 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Fri, 12 Jun 2015 23:21:54 +0200
Subject: [PATCH] Added a test .yaml for Single Channel data
---
.../timelapse/SingleChannel.yaml | 189 ++++++++++++++++++
1 file changed, 189 insertions(+)
create mode 100755 spim_registration/timelapse/SingleChannel.yaml
diff --git a/spim_registration/timelapse/SingleChannel.yaml b/spim_registration/timelapse/SingleChannel.yaml
new file mode 100755
index 0000000..60b1688
--- /dev/null
+++ b/spim_registration/timelapse/SingleChannel.yaml
@@ -0,0 +1,189 @@
+common: {
+ # directory that contains the bean shell scripts
+ bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
+ directory_cuda: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/lib/",
+ fiji-app: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/ImageJ-linux64",
+ fiji-prefix: "/sw/bin/xvfb-run -a",
+ first_xml_filename: "test_unicore",
+ hdf5_xml_filename: '"hdf5_test_unicore"',
+ merged_xml: "hdf5_test_unicore_merge",
+ ntimepoints: 5,
+ angles: "0,72,144,216,288",
+ channels: "green",
+ illumination: "0",
+ pixel_distance_x: '0.28590106964',
+ pixel_distance_y: '0.28590106964',
+ pixel_distance_z: '1.50000',
+ pixel_unit: "um",
+ # transformation_switch: "timelapse_dublicate",
+ transformation_switch: "timelapse",
+ # fusion_switch: "deconvolution"
+ fusion_switch: "fusion"
+ }
+
+define_xml_czi: {
+ first_czi: "2015-04-11_LZ2_Stock68_3.czi",
+ rotation_around: "X-Axis",
+ bsh_file: "define_czi.bsh"
+ }
+
+define_xml_tif: {
+ image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif',
+ imglib_container: '"ArrayImg (faster)"',
+ multiple_angles: '"YES (one file per angle)"',
+ multiple_channels: '"NO (one channel)"',
+ multiple_illumination_directions: '"NO (one illumination direction)"',
+ multiple_timepoints: '"YES (one file per time-point)"',
+ type_of_dataset: '"Image Stacks (ImageJ Opener)"',
+ bsh_file: "define_tif_zip.bsh"
+ }
+
+resave_hdf5: {
+ hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"',
+ resave_angle: '"All angles"',
+ resave_channel: '"All channels"',
+ resave_illumination: '"All illuminations"',
+ resave_timepoint: '"All Timepoints"',
+ setups_per_partition: '0',
+ subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"',
+ timepoints_per_partition: '1',
+ bsh_file: "export.bsh"
+ }
+
+registration: {
+ # "Single Channel" is not a valid choice for "Process_channel"
+ reg_process_channel: '"All channels"',
+ reg_processing_channel: '"green"',
+ reg_interest_points_channel: '"beads"',
+ reg_radius_1: '2',
+ reg_radius_2: '3',
+ reg_threshold: '0.005',
+ initial_sigma: '1.8',
+ threshold_gaussian: '0.0080',
+ type_of_detection: '"Difference-of-Mean (Integral image based)"',
+ label_interest_points: '"beads"',
+ reg_process_timepoint: '"Single Timepoint (Select from List)"',
+ reg_process_angle: '"All angles"',
+ reg_process_illumination: '"All illuminations"',
+ subpixel_localization: '"3-dimensional quadratic fit"',
+ detection_min_max: "find_maxima",
+ type_of_registration: '"Register timepoints individually"',
+ algorithm: '"Fast 3d geometric hashing (rotation invariant)"',
+ transformation_model: "Affine",
+ allowed_error_for_ransac: '5',
+ significance: '10',
+ fix_tiles: '"Fix first tile"',
+ map_back_tiles: '"Map back to first tile using rigid model"',
+ model_to_regularize_with: "Rigid",
+ lambda: '0.10',
+ imglib_container: '"ArrayImg (faster)"',
+ bsh_file: "registration.bsh"
+ }
+
+xml_merge: {
+ bsh_file: "xml_merge.bsh"
+ }
+
+timelapse: {
+ reference_timepoint: '0',
+ type_of_registration_timelapse: '"Match against one reference timepoint (no global optimization)"',
+ timelapse_process_timepoints: '"All Timepoints"',
+ bsh_file: "timelapse_registration.bsh"
+ }
+
+Dublicate_transformations: {
+ source_dublication: "red",
+ target_dublication: "green",
+ duplicate_which_transformations: '"Replace all transformations"',
+ bsh_file: "Dublicate_transformations.bsh"
+ }
+
+fusion: {
+ bsh_file: "fusion.bsh",
+ downsample: '4',
+ fused_image: '"Append to current XML Project"',
+ imglib2_container_fusion: '"ArrayImg"',
+ imglib2_data_container: '"ArrayImg (faster)"',
+ interpolation: '"Linear Interpolation"',
+ minimal_x: '190',
+ minimal_y: '-16',
+ minimal_z: '-348',
+ maximal_x: '1019',
+ maximal_y: '1941',
+ maximal_z: '486',
+ pixel_type: '"16-bit unsigned integer"',
+ process_angle: '"All angles"',
+ process_channel: '"All channels"',
+ process_illumination: '"All illuminations"',
+ process_timepoint: '"Single Timepoint (Select from List)"',
+ process_views_in_paralell: '"All"',
+ xml_output: '"Save every XML with user-provided unique id"'
+ }
+
+external_transform: {
+ # channel setting: '"all_channels"'
+ channel_setting: '"green"',
+ transform_timepoint: '"All Timepoints"',
+ transform_angle: '"All angles"',
+ transform_channel: '"All channels"',
+ # illumination setting only one illumination side
+ transform_illumination: '"All illuminations"',
+ 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"',
+ transformation: '"Rigid"',
+ bsh_file: "transform.bsh"
+ }
+
+deconvolution: {
+ iterations: '1',
+ minimal_x_deco: '190',
+ minimal_y_deco: '-16',
+ minimal_z_deco: '-348',
+ maximal_x_deco: '1019',
+ maximal_y_deco: '1941',
+ maximal_z_deco: '486',
+ detections_to_extract_psf_for_channel: '"beads"',
+ process_timepoint: '"Single Timepoint (Select from List)"',
+ process_angle: '"All angles"',
+ process_channel: '"All channels"',
+ process_illumination: '"All illuminations"',
+ Tikhonov_parameter: '0.0006',
+ compute: '"in 512x512x512 blocks"',
+ compute_on: '"GPU (Nvidia CUDA via JNA)"',
+ imglib2_container: '"ArrayImg"',
+ osem_acceleration: '"1 (balanced)"',
+ psf_estimation: '"Extract from beads"',
+ psf_size_x: '19',
+ psf_size_y: '19',
+ psf_size_z: '25',
+ type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"',
+ bsh_file: "deconvolution_GPU.bsh"
+ }
+
+hdf5_output: {
+ output_image_file_pattern: 'TP{{t}}_Chgreen_Ill0_Ang0,72,144,216,288.tif',
+ output_xml: '"fused_Single_Channel"',
+ output_hdf5_xml: '"hdf5_fused_Single_Channel"',
+ output_multiple_channels: '"NO (one channel)"',
+ output_timepoints: '0-4',
+ output_pixel_distance_x: 0.5718,
+ output_pixel_distance_y: 0.5718,
+ output_pixel_distance_z: 0.5718,
+ output_pixel_unit: 'um',
+ output_channels: "green",
+ output_data_type: "32Bit",
+ convert_32bit: '"[Use min/max of first image (might saturate intenities over time)]"',
+ output_type_of_dataset: '"Image Stacks (ImageJ Opener)"',
+ 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)"',
+ subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}}, {{4,4,4}}, {{8,8,8}} }}"',
+ chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}}, {{16,16,16}}, {{16,16,16}} }}"',
+ # subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}} }}"',
+ # chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}} }}"',
+ bsh_file_define: "define_output.bsh",
+ bsh_file_hdf5: "export_output.bsh"
+ }
+
--
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