How to fuse in Fiji Macro using the "default" bounding box

[Xqua]

Hi, I'm curious on how I can make a run() statement for the fusion that will take the default bounding box that is "offered" in the BDV selection.

Basically I have a lot (90+) dataset of fixed embryos and I'm trying to automate the process instead of clicking through it 90+ times.

I know how to do it for timelapses, but not for different dataset.

So far I'm here (aka I can run the define CZI detection and registration) But I can't seem to find a parameter set for fusion that will let me run it without a popup OR a pre defined bounding box.

Thanks !

// "BatchProcessFolders"
//

   dir = getDirectory("Choose a Directory ");
   setBatchMode(true);
   count = 0;
   countFiles(dir);
   n = 0;
   processFiles(dir);
   //print(count+" files processed");

   function countFiles(dir) {
      list = getFileList(dir);
      for (i=0; i<list.length; i++) {
          if (endsWith(list[i], "/"))
              countFiles(""+dir+list[i]);
          else
              count++;
      }
  }

   function processFiles(dir) {
      list = getFileList(dir);
      for (i=0; i<list.length; i++) {
          if (endsWith(list[i], "/"))
              processFiles(""+dir+list[i]);
          else {
             showProgress(n++, count);
             path = dir+list[i];
             processFile(path);
          }
      }
  }

  function processFile(path) {
       if (endsWith(path, ".czi")) {
           name = File.getName(path);
           name = substring(name, 0, lastIndexOf(name, “.”));
           params = "type_of_dataset=[Zeiss Lightsheet Z.1 Dataset (LOCI Bioformats)] xml_filename=";
           params += name;
           params += ".xml browse=";
           params += path;
           params += " first_czi=";
           params += path;
           params += " angle_1=0 angle_2=90 angle_3=180 angle_4=270 channel_1=405 channel_2=561 channel_3=488 channel_4=638 _______illumination_1=0 apply_rotation_to_dataset fix_bioformats";
           run("Define Multi-View Dataset", params);

           xml_path = substring(path, 0, lastIndexOf(path, “/”)) + "dataset.xml";
           params = "select_xml=" + xml_path + " process_angle=[All angles] process_channel=[Single channel (Select from List)] process_illumination=[All illuminations] process_timepoint=[All Timepoints] processing_channel=[channel 488] type_of_interest_point_detection=Difference-of-Gaussian label_interest_points=beads downsample_images subpixel_localization=[3-dimensional quadratic fit] interest_point_specification=[Weak & small (beads)] downsample_xy=[Match Z Resolution (less downsampling)] downsample_z=2x compute_on=[CPU (Java)]";
           run("Detect Interest Points for Registration", params);

           params = "select_xml=" + xml_path +  process_angle=[All angles] process_illumination=[All illuminations] process_timepoint=[All Timepoints] registration_algorithm=[Fast 3d geometric hashing (rotation invariant)] type_of_registration=[Register timepoints individually] interest_points_channel_405=[(DO NOT register this channel)] interest_points_channel_561=[(DO NOT register this channel)] interest_points_channel_488=beads interest_points_channel_638=[(DO NOT register this channel)] fix_tiles=[Fix first tile] map_back_tiles=[Do not map back (use this if tiles are fixed)] transformation=Affine regularize_model model_to_regularize_with=Rigid lamba=0.10 allowed_error_for_ransac=5 significance=10";
           run("Register Dataset based on Interest Points", params);

      }
  }

[StephanPreibisch]

Hi, I can record it with the macro recorder like that:

run("Fuse dataset ...", "select=/Users/spreibi/Documents/Microscopy/SPIM/HisYFP-SPIM/dataset.xml process_angle=[All angles] process_channel=[All channels] process_illumination=[All illuminations] process_tile=[All tiles] process_timepoint=[All Timepoints] bounding_box=[All Views] downsampling=13 pixel_type=[32-bit floating point] interpolation=[Linear Interpolation] image=[Precompute Image] blend produce=[Each timepoint & channel] fused_image=[Display using ImageJ]");

[StephanPreibisch]

the important part is: "bounding_box=[All Views]"

[Xqua]

That is great ! I could not find this somehow ... Thanks a lot !On Aug 2, 2018 2:36 PM, Stephan Preibisch notifications@github.com wrote:the important part is: "bounding_box=[All Views]"

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[Xqua]

Hi @StephanPreibisch

I'm getting an "All views" is not a valid option error

What Macro language are you using ? (If I record my macros I also do not get a "Fuse dataset ..." I get a "Fuse/Deconvolve Dataset")