Merge pull request #185 from ttngu207/main

make output_dir if not exist for task_mode="trigger" & update ScanInfo for mesocans

CHANGELOG.md

@@ -3,6 +3,11 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.9.4] - 2024-02-05
+
++ Fix - bugfix ingesting field xyz for mesoscan (multiROI) from ScanImage
++ Update - make `output_dir` if not exist for `task_mode="trigger"`
+
 ## [0.9.3] - 2024-01-29
 
 + Update - DataJoint Elements to install from GitHub instead of PyPI

element_calcium_imaging/imaging.py

@@ -372,7 +372,18 @@ def make(self, key):
             ProcessingTask.update1(
                 {**key, "processing_output_dir": output_dir.as_posix()}
             )
-        output_dir = find_full_path(get_imaging_root_data_dir(), output_dir).as_posix()
+
+        try:
+            output_dir = find_full_path(
+                get_imaging_root_data_dir(), output_dir
+            ).as_posix()
+        except FileNotFoundError as e:
+            if task_mode == "trigger":
+                processed_dir = pathlib.Path(get_processed_root_data_dir())
+                output_dir = processed_dir / output_dir
+                output_dir.mkdir(parents=True, exist_ok=True)
+            else:
+                raise e
 
         if task_mode == "load":
             method, imaging_dataset = get_loader_result(key, ProcessingTask)

element_calcium_imaging/imaging_no_curation.py

@@ -373,7 +373,18 @@ def make(self, key):
             ProcessingTask.update1(
                 {**key, "processing_output_dir": output_dir.as_posix()}
             )
-        output_dir = find_full_path(get_imaging_root_data_dir(), output_dir).as_posix()
+
+        try:
+            output_dir = find_full_path(
+                get_imaging_root_data_dir(), output_dir
+            ).as_posix()
+        except FileNotFoundError as e:
+            if task_mode == "trigger":
+                processed_dir = pathlib.Path(get_processed_root_data_dir())
+                output_dir = processed_dir / output_dir
+                output_dir.mkdir(parents=True, exist_ok=True)
+            else:
+                raise e
 
         if task_mode == "load":
             method, imaging_dataset = get_loader_result(key, ProcessingTask)

element_calcium_imaging/imaging_preprocess.py

@@ -562,7 +562,18 @@ def make(self, key):
             ProcessingTask.update1(
                 {**key, "processing_output_dir": output_dir.as_posix()}
             )
-        output_dir = find_full_path(get_imaging_root_data_dir(), output_dir).as_posix()
+
+        try:
+            output_dir = find_full_path(
+                get_imaging_root_data_dir(), output_dir
+            ).as_posix()
+        except FileNotFoundError as e:
+            if task_mode == "trigger":
+                processed_dir = pathlib.Path(get_processed_root_data_dir())
+                output_dir = processed_dir / output_dir
+                output_dir.mkdir(parents=True, exist_ok=True)
+            else:
+                raise e
 
         if task_mode == "load":
             method, imaging_dataset = get_loader_result(key, ProcessingTask)

element_calcium_imaging/scan.py

@@ -201,7 +201,7 @@ class ScanInfo(dj.Imported):
         nfields (int): Number of fields.
         nchannels (int): Number of channels.
         ndepths (int): Number of scanning depths (planes).
-        nframes (int): Number of recorded frames.
+        nframes (int): Number of recorded frames (time steps).
         nrois (int): Number of ROIs (see scanimage's multi ROI imaging).
         x (float, optional): ScanImage's 0 point in the motor coordinate system (um).
         y (float, optional): ScanImage's 0 point in the motor coordinate system (um).
@@ -222,7 +222,7 @@ class ScanInfo(dj.Imported):
     nfields              : tinyint   # number of fields
     nchannels            : tinyint   # number of channels
     ndepths              : int       # Number of scanning depths (planes)
-    nframes              : int       # number of recorded frames
+    nframes              : int       # number of recorded frames (time steps)
     nrois                : tinyint   # number of ROIs (see scanimage's multi ROI imaging)
     x=null               : float     # (um) ScanImage's 0 point in the motor coordinate system
     y=null               : float     # (um) ScanImage's 0 point in the motor coordinate system
@@ -296,59 +296,53 @@ def make(self, key):
             import scanreader
 
             # Read the scan
-            scan = scanreader.read_scan(scan_filepaths)
+            scan_ = scanreader.read_scan(scan_filepaths)
 
             # Insert in ScanInfo
-            x_zero, y_zero, z_zero = scan.motor_position_at_zero or (None, None, None)
+            x_zero, y_zero, z_zero = scan_.motor_position_at_zero or (None, None, None)
 
             self.insert1(
                 dict(
                     key,
-                    nfields=scan.num_fields,
-                    nchannels=scan.num_channels,
-                    nframes=scan.num_frames,
-                    ndepths=scan.num_scanning_depths,
+                    nfields=scan_.num_fields,
+                    nchannels=scan_.num_channels,
+                    nframes=scan_.num_frames,
+                    ndepths=scan_.num_scanning_depths,
                     x=x_zero,
                     y=y_zero,
                     z=z_zero,
-                    fps=scan.fps,
-                    bidirectional=scan.is_bidirectional,
-                    usecs_per_line=scan.seconds_per_line * 1e6,
-                    fill_fraction=scan.temporal_fill_fraction,
-                    nrois=scan.num_rois if scan.is_multiROI else 0,
-                    scan_duration=scan.num_frames / scan.fps,
+                    fps=scan_.fps,
+                    bidirectional=scan_.is_bidirectional,
+                    usecs_per_line=scan_.seconds_per_line * 1e6,
+                    fill_fraction=scan_.temporal_fill_fraction,
+                    nrois=scan_.num_rois if scan_.is_multiROI else 0,
+                    scan_duration=scan_.num_frames / scan_.fps,
                 )
             )
             # Insert Field(s)
-            if scan.is_multiROI:
+            if scan_.is_multiROI:
                 self.Field.insert(
                     [
                         dict(
                             key,
                             field_idx=field_id,
-                            px_height=scan.field_heights[field_id],
-                            px_width=scan.field_widths[field_id],
-                            um_height=scan.field_heights_in_microns[field_id],
-                            um_width=scan.field_widths_in_microns[field_id],
+                            px_height=scan_.field_heights[field_id],
+                            px_width=scan_.field_widths[field_id],
+                            um_height=scan_.field_heights_in_microns[field_id],
+                            um_width=scan_.field_widths_in_microns[field_id],
                             field_x=(
-                                x_zero
-                                + scan._degrees_to_microns(scan.fields[field_id].x)
-                                if x_zero
-                                else None
+                                (x_zero or 0)
+                                + scan_._degrees_to_microns(scan_.fields[field_id].x)
                             ),
                             field_y=(
-                                y_zero
-                                + scan._degrees_to_microns(scan.fields[field_id].y)
-                                if y_zero
-                                else None
-                            ),
-                            field_z=(
-                                z_zero + scan.fields[field_id].depth if z_zero else None
+                                (y_zero or 0)
+                                + scan_._degrees_to_microns(scan_.fields[field_id].y)
                             ),
-                            delay_image=scan.field_offsets[field_id],
-                            roi=scan.field_rois[field_id][0],
+                            field_z=((z_zero or 0) + scan_.fields[field_id].depth),
+                            delay_image=scan_.field_offsets[field_id],
+                            roi=scan_.field_rois[field_id][0],
                         )
-                        for field_id in range(scan.num_fields)
+                        for field_id in range(scan_.num_fields)
                     ]
                 )
             else:
@@ -357,20 +351,20 @@ def make(self, key):
                         dict(
                             key,
                             field_idx=plane_idx,
-                            px_height=scan.image_height,
-                            px_width=scan.image_width,
-                            um_height=getattr(scan, "image_height_in_microns", None),
-                            um_width=getattr(scan, "image_width_in_microns", None),
+                            px_height=scan_.image_height,
+                            px_width=scan_.image_width,
+                            um_height=getattr(scan_, "image_height_in_microns", None),
+                            um_width=getattr(scan_, "image_width_in_microns", None),
                             field_x=x_zero if x_zero else None,
                             field_y=y_zero if y_zero else None,
                             field_z=(
-                                z_zero + scan.scanning_depths[plane_idx]
+                                z_zero + scan_.scanning_depths[plane_idx]
                                 if z_zero
                                 else None
                             ),
-                            delay_image=scan.field_offsets[plane_idx],
+                            delay_image=scan_.field_offsets[plane_idx],
                         )
-                        for plane_idx in range(scan.num_scanning_depths)
+                        for plane_idx in range(scan_.num_scanning_depths)
                     ]
                 )
         elif acq_software == "Scanbox":

element_calcium_imaging/version.py

@@ -1,3 +1,3 @@
 """Package metadata."""
 
-__version__ = "0.9.3"
+__version__ = "0.9.4"