adding NWB loading support

rastermap/gui/gui.py

@@ -293,15 +293,15 @@ def dropEvent(self, event):
         file = files[0]
         file0, ext = os.path.splitext(file)
         proc_file = file0 + "_embedding.npy"
-        if ext == ".npy" or ext == ".mat" or ext==".npz":
+        if ext == ".npy" or ext == ".mat" or ext==".npz" or ext==".nwb":
             if file[-14:] == "_embedding.npy":
                 io.load_proc(self, name=files[0])
             elif os.path.exists(proc_file):
                 io.load_proc(self, name=proc_file)
             else:
                 io.load_mat(self, name=files[0])
         else:
-            print("ERROR: must drag and drop *.npy, *.npz, or *.mat files")
+            print("ERROR: must drag and drop *.npy, *.npz, *.nwb or *.mat files")
 
     def plane_window(self):
         self.PlaneWindow = views.PlaneWindow(self)
@@ -598,37 +598,39 @@ def plot_neuron_pos(self, init=False, roi_id=None):
             self.update_status_bar("ERROR: please upload neuron position data")
 
     def plot_scatter(self, x, y, roi_id=None, iplane=0):
-        subsample = 1
+        subsample = max(1, int(len(x)/5000))
+        n_pts = len(x) // subsample
+        marker_size = int(3 * max(1, 800 / n_pts))
         if self.all_neurons_checkBox.isChecked() and roi_id is None:
             colors = colormaps.gist_ncar[np.linspace(
                 0, 254, len(x)).astype("int")][self.sorting]
             brushes = [pg.mkBrush(color=c) for c in colors[::subsample]]
             self.scatter_plots[iplane][0].setData(x[::subsample], y[::subsample], 
-                                                  symbol="o", size=3,
+                                                  symbol="o", size=marker_size,
                                                   brush=brushes,
                                                   hoverable=True)
             for i in range(1, nclust_max + 1):
                 self.scatter_plots[iplane][i].setData([], [])
         else:
             if roi_id is None:
                 self.scatter_plots[iplane][0].setData(
-                    x, y, symbol="o", size=3,
+                    x, y, symbol="o", size=marker_size,
                     brush=pg.mkBrush(color=(180, 180, 180)),
                     hoverable=True)
                 for roi_id in range(nclust_max):
                     if roi_id < len(self.cluster_rois):
                         selected = self.neurons_selected(self.cluster_slices[roi_id])
                         self.scatter_plots[iplane][roi_id + 1].setData(
                             x[selected][::subsample], y[selected][::subsample], 
-                            symbol="o", size=3,
+                            symbol="o", size=marker_size,
                             brush=pg.mkBrush(color=self.colors[roi_id][:3]),
                             hoverable=True)
                     else:
                         self.scatter_plots[iplane][roi_id + 1].setData([], [])
             else:
                 selected = self.neurons_selected(self.cluster_slices[roi_id])
                 self.scatter_plots[iplane][roi_id + 1].setData(
-                    x[selected], y[selected], symbol="o", size=3,
+                    x[selected], y[selected], symbol="o", size=marker_size,
                     brush=pg.mkBrush(color=self.colors[roi_id][:3]), hoverable=True)
 
 

rastermap/gui/io.py

@@ -4,7 +4,7 @@
 import os
 import numpy as np
 from qtpy import QtGui, QtCore, QtWidgets
-from qtpy.QtWidgets import QFileDialog, QMainWindow, QApplication, QWidget, QScrollBar, QSlider, QComboBox, QGridLayout, QPushButton, QFrame, QCheckBox, QLabel, QProgressBar, QLineEdit, QMessageBox, QGroupBox
+from qtpy.QtWidgets import QFileDialog, QInputDialog, QMainWindow, QApplication, QWidget, QScrollBar, QSlider, QComboBox, QGridLayout, QPushButton, QFrame, QCheckBox, QLabel, QProgressBar, QLineEdit, QMessageBox, QGroupBox
 import pyqtgraph as pg
 from scipy.stats import zscore
 import scipy.io as sio
@@ -64,8 +64,8 @@ def load_mat(parent, name=None):
     
     """
     if name is None:
-        name = QFileDialog.getOpenFileName(parent, "Open *.npy or *.mat",
-                                            filter="*.npy *.npz *.mat")
+        name = QFileDialog.getOpenFileName(parent, "Open *.npy, *.npz, *.nwb or *.mat",
+                                            filter="*.npy *.npz *.mat *.nwb")
         parent.fname = name[0]
         parent.filebase = name[0]
     else:
@@ -74,7 +74,28 @@ def load_mat(parent, name=None):
 
     X, Usv, Vsv, xy = load_activity(parent.fname)
     _load_activity_gui(parent, X, Usv, Vsv, xy)
-
+
+#def load_dandiset(parent, name=None):
+#    try:
+#        import fsspec
+#        import dandi
+#        import pynwb
+#        import aiohttp
+#    except:
+#        raise ImportError("fsspec, dandi, pynwb, and/or aiohttp not installed, please 'pip install fsspec dandi pynwb aiohttp'")
+#    if name is None:
+#        name, ok = QInputDialog().getText(parent, "QInputDialog().getText()",
+#                                     "Dandiset ID:", QLineEdit.Normal)
+#        if not (name and ok):
+#            raise ValueError("not input by user")
+#    
+#    fs = fsspec.filesystem("http")
+
+    #X, Usv, Vsv, xy = load_activity(parent.fname)
+    #_load_activity_gui(parent, X, Usv, Vsv, xy)
+
+
+
 def _load_sp(parent):
     if parent.n_samples < 100:
         smooth = 1

rastermap/io.py

@@ -116,6 +116,8 @@ def load_activity(filename):
         dat = np.load(filename, allow_pickle=True)
         keys = dat.files
         X, Usv, Vsv, xy = _load_dict(dat, keys)    
+    elif ext == ".nwb":
+        X, xy = _load_nwb(filename)
     else:
         raise Exception("Invalid file type")
 
@@ -147,6 +149,78 @@ def load_activity(filename):
 
     return X, Usv, Vsv, xy
 
+
+def _cell_center(voxel_mask):
+    x = np.median(np.array([v[0] for v in voxel_mask]))
+    y = np.median(np.array([v[1] for v in voxel_mask]))
+    return np.array([x, y])
+
+def _load_nwb(filename):
+    try:
+        from pynwb import NWBHDF5IO, NWBFile, TimeSeries
+        from pynwb.ophys import (
+            DfOverF,
+            Fluorescence  ,
+            RoiResponseSeries      
+        )
+    except:
+        raise ImportError("pynwb not installed, please pip install pynwb")
+    """ load ophys data from nwb"""
+    with NWBHDF5IO(filename, "r") as io:
+        read_nwbfile = io.read()
+
+        # load neural activity
+        X = [x for x in read_nwbfile.objects.values() if isinstance(x, Fluorescence)]
+        names = [x.name for x in read_nwbfile.objects.values() if isinstance(x, Fluorescence)]
+        if len(X) == 0:
+            X = [x for x in read_nwbfile.objects.values() if isinstance(x, DfOverF)]
+            names = [x.name for x in read_nwbfile.objects.values() if isinstance(x, DfOverF)]
+            if len(X) == 0:
+                X = [x for x in read_nwbfile.objects.values() if isinstance(x, RoiResponseSeries)]
+                names = [x.name for x in read_nwbfile.objects.values() if isinstance(x, RoiResponseSeries)]
+
+
+        if len(X) > 0:
+            if len(X) == 3 and "Deconvolved" in names:
+                X = X[names.index("Deconvolved")]
+            elif len(X) > 1:
+                # todo: allow user to select series
+                print(f"more than one series to choose from, taking first series {names[0]}")
+                X = X[0]
+            elif len(X) == 1:
+                X = X[0]
+
+            planes = list(X.roi_response_series.keys())
+
+            spks = np.concatenate(([X[plane].data[:] for plane in planes]), 
+                                    axis=1).T 
+            spks = spks.astype("float32")
+            ids = np.concatenate(([X[plane].rois.data[:] for plane in planes]), 
+                                    axis=0)
+
+            if hasattr(X[planes[0]].rois[0], "image_mask"):
+                roikey = "image_mask"
+            elif hasattr(X[planes[0]].rois[0], "voxel_mask"):
+                roikey = "voxel_mask"
+            else:
+                roikey = None
+
+            if roikey is not None:
+                xy = np.concatenate([np.array([_cell_center(roi[roikey].values[0]) 
+                                            for roi in X[plane].rois]) 
+                                                for plane in planes])
+            else:
+                voxel_masks = np.concatenate([np.array([roi
+                                        for roi in X[plane].rois]) 
+                                            for plane in planes])
+                xy = np.stack([_cell_center(vm[0][0]) for vm in voxel_masks], 
+                                        axis=0)
+        else:
+            raise ValueError("not an ophys NWB file with a Fluorescence or DfOverF roi_response_series")
+
+    return spks, xy
+
+
 def _load_iscell(filename):
     basename = os.path.split(filename)[0]
     try: