Add multi_tiff attribute for Bruker scans

kushalbakshi · Apr 23, 2024 · 18d0e34 · 18d0e34
1 parent bf76438
commit 18d0e34
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Showing 2 changed files with 19 additions and 11 deletions.
diff --git a/element_calcium_imaging/field_processing.py b/element_calcium_imaging/field_processing.py
@@ -1,5 +1,6 @@
 import importlib
 import inspect
+import shutil
 import pathlib
 from collections.abc import Callable
 from datetime import datetime
@@ -74,7 +75,7 @@ def key_source(self):
             * scan.ScanInfo.proj("nrois", "nfields")
             * imaging.ProcessingParamSet.proj("processing_method")
             & "task_mode = 'trigger'"
-        ) & "nfields > 1"
+        ) & "nfields >= 1"
         ks &= "(processing_method = 'suite2p' AND nrois > 0) OR (processing_method = 'caiman' AND nrois = 0)"
         return ks - imaging.Processing.proj()
 
@@ -105,9 +106,9 @@ def make(self, key):
         acq_software = (scan.Scan & key).fetch1("acq_software")
 
         field_ind = (scan.ScanInfo.Field & key).fetch("field_idx")
-        sampling_rate, ndepths, nchannels, nfields, nrois = (
+        sampling_rate, ndepths, nchannels, nfields, nrois, multi_tiff = (
             scan.ScanInfo & key
-        ).fetch1("fps", "ndepths", "nchannels", "nfields", "nrois")
+        ).fetch1("fps", "ndepths", "nchannels", "nfields", "nrois", "multi_tiff")
 
         if method == "caiman" and acq_software == "PrairieView":
             from element_interface.prairie_view_loader import (
@@ -132,14 +133,18 @@ def make(self, key):
                 prepared_input_dir = output_dir.parent / "prepared_input"
                 prepared_input_dir.mkdir(exist_ok=True)
 
-                image_files = [
-                    PVmeta.write_single_bigtiff(
-                        plane_idx=plane_idx,
-                        channel=channel,
-                        output_dir=prepared_input_dir,
-                        caiman_compatible=True,
-                    )
-                ]
+                if multi_tiff:
+                    shutil.copy(find_full_path(scan.get_imaging_root_data_dir(), image_file), prepared_input_dir)
+                    image_files = [prepared_input_dir / pathlib.Path(image_file).name]
+                else:
+                    image_files = [
+                        PVmeta.write_single_bigtiff(
+                            plane_idx=plane_idx,
+                            channel=channel,
+                            output_dir=prepared_input_dir,
+                            caiman_compatible=True,
+                        )
+                    ]
 
                 field_processing_tasks.append(
                     {

diff --git a/element_calcium_imaging/scan.py b/element_calcium_imaging/scan.py
@@ -214,6 +214,7 @@ class ScanInfo(dj.Imported):
         scan_datetime (datetime, optional): Datetime of the scan.
         scan_duration (float, optional): Duration of the scan (s).
         bidirectional_z (bool, optional): True = bidirectional z-scan.
+        multi_tiff (bool): True = multi-tiff scan. Relevant for Bruker PrairieView.
     """
 
     definition = """ # General data about the resoscans/mesoscans from header
@@ -234,6 +235,7 @@ class ScanInfo(dj.Imported):
     scan_datetime=null   : datetime  # datetime of the scan
     scan_duration=null   : float     # (seconds) duration of the scan
     bidirectional_z=null : boolean   # true = bidirectional z-scan
+    multi_tiff=True      : boolean   # true = multi-tiff scan. Relevant for Bruker PrairieView
     """
 
     class Field(dj.Part):
@@ -547,6 +549,7 @@ def estimate_nd2_scan_duration(nd2_scan_obj):
                     usecs_per_line=PVScan_info["usecs_per_line"],
                     scan_datetime=PVScan_info["scan_datetime"],
                     scan_duration=PVScan_info["scan_duration"],
+                    multi_tiff=PVScan_info["multi_tiff"],
                 )
             )