Merge pull request #65 from SilverLabUCL/replace_manifold

replace deprecated ImagingPlane parameters

setup.py

@@ -52,7 +52,7 @@ def read(*names, **kwargs):
         # eg: 'keyword1', 'keyword2', 'keyword3',
     ],
     install_requires=[
-        'pynwb==1.2.1',
+        'pynwb==1.3.2',
         'appdirs',
         'h5py>=2.7.1',
         'hdmf<2.0.0',

src/silverlabnwb/nwb_file.py

@@ -808,15 +808,15 @@ def _write_roi_data(self, all_rois, num_trials, cycles_per_trial,
         # Quick fix...
         self.nwb_io.close()
 
-    def add_imaging_plane(self, name, manifold, description,
+    def add_imaging_plane(self, name, description, origin_coords, grid_spacing,
                           green=True, red=True):
         """Add a new imaging plane definition to /general/optophysiology.
 
         :param name: A name for the NWB group representing this imaging plane.
-        :param manifold: 3d array giving the x,y,z coordinates in microns for each pixel
-            in the plane. If the plane is really a line, this can be an Nx1x3 array.
         :param description: Brief text description of the plane, e.g. "Reference Z stack",
             "Pointing mode acquisition sequence".
+        :param origin_coords: physical location of the first element of the imaging plane
+        :param grid_spacing: distance along each axis between two adjacent pixels in the plane (assumes a regular grid)
         :param green: Whether to include the green channel.
         :param red: Whether to include the red channel.
         """
@@ -833,13 +833,6 @@ def add_imaging_plane(self, name, manifold, description,
                                      description='Red channel, typically used for reference.',
                                      emission_lambda=float(opto_metadata['emission_lambda']['red']))
             channels.append(channel)
-        if self.compress:
-            wrapped_manifold = H5DataIO(data=manifold,
-                                        compression='gzip',
-                                        compression_opts=4,
-                                        )
-        else:
-            wrapped_manifold = manifold
         for channel in channels:
             self.nwb_file.create_imaging_plane(
                 name="{}_{}".format(name, channel.name),
@@ -850,9 +843,10 @@ def add_imaging_plane(self, name, manifold, description,
                 imaging_rate=cycle_rate,
                 indicator=opto_metadata['calcium_indicator'],
                 location=opto_metadata['location'],
-                manifold=wrapped_manifold,
-                unit='metre',
-                conversion=1e6,
+                origin_coords=origin_coords,
+                origin_coords_unit='micrometers',
+                grid_spacing=grid_spacing,
+                grid_spacing_unit='micrometers',
                 reference_frame='TODO: In lab book (partly?)'
             )
 
@@ -876,22 +870,19 @@ def read_zplane(self, zplane_path):
             index_col=False)
         num_pixels = self.imaging_info.frame_size
         plane_width_in_microns = self.imaging_info.field_of_view
-        template_manifold = np.zeros((num_pixels, num_pixels, 3))
-        x = np.linspace(0, plane_width_in_microns, num_pixels)
-        y = np.linspace(0, plane_width_in_microns, num_pixels)
-        xv, yv = np.meshgrid(x, y)
-        template_manifold[:, :, 0] = xv
-        template_manifold[:, :, 1] = yv
         self.zplanes = {}
         for plane in zplane_data.itertuples():
-            manifold = template_manifold.copy()
-            manifold[:, :, 2] = plane.z
             name = 'Zstack{:04d}'.format(plane.Index + 1)
             self.zplanes[plane.z] = name
+            # TODO: Is it OK to have 2D spacing with 3D coords (allowed by pynwb, but this doesn't mean it's OK)?
+            spacing = plane_width_in_microns / (num_pixels - 1)
+            origin_coords = [0, 0, plane.z]
             self.add_imaging_plane(
                 name=name,
                 description='Reference Z stack',
-                manifold=manifold)
+                origin_coords=origin_coords,
+                grid_spacing=np.float32([spacing, spacing, 0])
+            )
         ZplanePockelsDatasetClass = get_class('ZplanePockelsDataset', 'silverlab_extended_schema')
         self.custom_silverlab_dict['zplane_pockels'] = ZplanePockelsDatasetClass(
             columns=zplane_data.columns.tolist(),

tests/data/metadata_only_B.sig2

@@ -4,6 +4,12 @@ Generating signature for metadata_only_B.nwb
 	@.specloc: type=Reference val="->/specifications"
 /file_create_date: dtype=ignored shape=ignored val="ignored"
 /general/data_collection: dtype=object shape=() val="All about the data."
+/general/devices/AOL_microscope
+	@description: type=str val="Random access 3d acousto-optic lens two-photon microscope"
+/general/devices/air_puff_device
+	@description: type=str val="Delivers an air puff stimulus to the mouse's whiskers"
+/general/devices/mouse_wheel_device
+	@description: type=str val="Records mouse speed data"
 /general/experiment_description: dtype=object shape=() val="Experiment description"
 /general/experimenter: dtype=object shape=(1,) val="[B Y-S]"
 /general/institution: dtype=object shape=() val="University College London"