adding support for spike_times data in gui (#27)

Author: carsen-stringer

README.md

@@ -198,6 +198,18 @@ Most of the time you will input to `Rastermap().fit` a matrix of neurons by time
 * **itrain** : array, shape (n_features,) (optional, default None)
     fit embedding on timepoints itrain only
 
+If you have a `spike_times.npy` and `spike_clusters.npy`, create your time-binned data 
+matrix with, where the bin size `st_bin` is in milliseconds (assuming your spike times are in seconds):
+
+```
+from rastermap import io 
+
+# bin spike times into neurons by time matrix
+data = io.load_spike_times("spike_times.npy", "spike_clusters.npy", st_bin=100)
+```
+
+You can also load these matrices into the GUI with the `File > Load spike_times...` option.
+
 # Settings
 
 These are inputs to the `Rastermap` class initialization, the settings are sorted in order of importance 

rastermap/__main__.py

@@ -6,7 +6,7 @@
 import argparse
 import os
 from rastermap import Rastermap
-from rastermap.io import load_activity
+from rastermap.io import load_activity, load_spike_times
 
 try:
     from rastermap.gui import gui
@@ -24,15 +24,23 @@
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="spikes")
     parser.add_argument("--S", default=[], type=str, help="spiking matrix")
+    parser.add_argument("--spike_times", default=[], type=str, help="spike_times.npy")
+    parser.add_argument("--spike_clusters", default=[], type=str, help="spike_clusters.npy")
+    parser.add_argument("--st_bin", default=100, type=float, help="bin size in milliseconds for spike times")
     parser.add_argument("--proc", default=[], type=str,
                         help="processed data file 'embedding.npy'")
     parser.add_argument("--ops", default=[], type=str, help="options file 'ops.npy'")
     parser.add_argument("--iscell", default=[], type=str,
                         help="which cells to select for processing")
     args = parser.parse_args()
 
-    if len(args.ops) > 0 and len(args.S) > 0:
-        X, Usv, Vsv, xy = load_activity(args.S)
+    if len(args.ops) > 0 and (len(args.S) > 0 or 
+            (len(args.spike_times) > 0 and len(args.spike_clusters) > 0)):
+        if len(args.S) > 0:
+            X, Usv, Vsv, xy = load_activity(args.S)
+        else:
+            Usv, Vsv, xy = None, None, None 
+            X = load_spike_times(args.spike_times, args.spike_clusters, args.st_bin)
         ops = np.load(args.ops, allow_pickle=True).item()
         if len(args.iscell) > 0:
             iscell = np.load(args.iscell)
@@ -62,14 +70,16 @@
         model.fit(data=X, Usv=Usv, Vsv=Vsv)
 
         proc = {
-            "filename": args.S,
-            "save_path": os.path.split(args.S)[0],
+            "filename": args.S if len(args.S) > 0 else args.spike_times,
+            "filename_cluid": args.spike_clusters if args.spike_clusters else None,
+            "st_bin": args.st_bin if args.spike_clusters else None,
+            "save_path": os.path.split(args.S)[0] if args.S else os.path.split(args.spike_times)[0],
             "isort": model.isort,
             "embedding": model.embedding,
             "user_clusters": None,
             "ops": ops,
         }
-        basename, fname = os.path.split(args.S)
+        basename, fname = os.path.split(args.S) if args.S else os.path.split(args.spike_times)
         fname = os.path.splitext(fname)[0]
         try:
             np.save(os.path.join(basename, f"{fname}_embedding.npy"), proc)

rastermap/gui/gui.py

@@ -178,6 +178,7 @@ def __init__(self, filename=None, proc=False):
         # Default variables
         self.tpos = -0.5
         self.tsize = 1
+        self.from_spike_times = False
         self.reset_variables()
 
         self.init_time_roi()

rastermap/gui/io.py

@@ -4,12 +4,13 @@
 import os
 import numpy as np
 from qtpy import QtGui, QtCore, QtWidgets
-from qtpy.QtWidgets import QFileDialog, QInputDialog, QMainWindow, QApplication, QWidget, QScrollBar, QSlider, QComboBox, QGridLayout, QPushButton, QFrame, QCheckBox, QLabel, QProgressBar, QLineEdit, QMessageBox, QGroupBox
+from qtpy.QtWidgets import QFileDialog, QDialog, 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
+from scipy.sparse import csr_array
 import scipy.io as sio
 from . import guiparts
-from ..io import _load_iscell, _load_stat, load_activity
+from ..io import _load_iscell, _load_stat, load_activity, load_spike_times
 
 def _load_activity_gui(parent, X, Usv, Vsv, xy):
     parent.reset_variables()
@@ -54,6 +55,66 @@ def _load_activity_gui(parent, X, Usv, Vsv, xy):
     parent.sorting = np.arange(0, parent.n_samples).astype(np.int64)
     _load_sp(parent)
 
+
+class SpikeTimeLoad(QDialog):
+    def __init__(self, parent=None):
+        super().__init__()
+        self.parent = parent
+        self.layout = QGridLayout(self)
+        self.files, self.file_labels = [], []
+        lbl = ["spike_times", "spike_clusters"]
+        for j in range(2):
+            self.files.append(QPushButton(f"Choose {lbl[j]} file", self))
+            self.files[-1].clicked.connect(lambda state, idx=j: self.get_file(idx))
+            self.layout.addWidget(self.files[-1], j, 0, 1, 1)
+            self.file_labels.append(QLabel("", self))
+            self.layout.addWidget(self.file_labels[-1], j, 1, 1, 1)
+
+        # time bin size lineedit
+        self.time_bin = QLineEdit("100", self)
+        self.layout.addWidget(self.time_bin, 2, 1, 1, 1)
+        self.layout.addWidget(QLabel("Time bin size (in millisec.)", self), 2, 0, 1, 1)
+
+        # Submit button
+        self.submit_button = QPushButton("Submit", self)
+        self.submit_button.clicked.connect(self.submit)
+        self.layout.addWidget(self.submit_button, 3, 0, 1, 2)
+
+        self.setWindowTitle("spike time input")
+        self.show()
+
+    def get_file(self, j):
+        name = QFileDialog.getOpenFileName(self, "Open *.npy or *.mat",
+                                           filter="*.npy *.mat")
+        self.file_labels[j].setText(name[0])
+        
+    def submit(self):
+        if not self.file_labels[0].text() or not self.file_labels[1].text():
+            QMessageBox.critical(self, 'Error', 'Both files are required!')
+        else:
+            fname = self.file_labels[0].text()
+            fname_cluid = self.file_labels[1].text()
+            st_bin = float(self.time_bin.text())
+            st_bin = min(5000, max(5, st_bin))
+            print(f"setting bin size to {st_bin} for visualization")
+            _load_spike_times(self.parent, fname, fname_cluid, st_bin)
+
+def _load_spike_times(parent, fname, fname_cluid, st_bin):
+    spks = load_spike_times(fname, fname_cluid, st_bin)
+    parent.fname = fname 
+    parent.fname_cluid = fname_cluid
+    parent.st_bin = st_bin
+    parent.from_spike_times = True
+    _load_activity_gui(parent, spks, None, None, None)
+
+def load_st_clu(parent, name=None):
+    """ load spike times of neurons (*.npy or *.mat) """
+    if name is None:
+        st = SpikeTimeLoad(parent)
+        st.exec_()
+    
+
+        
 def load_mat(parent, name=None):
     """ load data matrix of neurons by time (*.npy or *.mat)
     
@@ -361,13 +422,27 @@ def load_proc(parent, name=None):
         else:
             print(f"ERROR: {parent.proc['filename']} not found")
             return
+        
+        if parent.proc["filename_cluid"]:
+            if os.path.exists(parent.proc["filename_cluid"]):
+                parent.fname_cluid = parent.proc["filename_cluid"]
+            elif os.path.exists(os.path.join(foldername, filename)):
+                parent.fname_cluid = os.path.join(foldername, filename)
+            else:
+                print(f"ERROR: {parent.proc['filename_cluid']} not found")
+                return
+            parent.st_bin = parent.proc["st_bin"]
+        
 
         isort = parent.proc["isort"]
         y = parent.proc["embedding"]
         ops = parent.proc["ops"]
         user_clusters = parent.proc.get("user_clusters", None)
-        
-        X, Usv, Vsv, xy = load_activity(parent.fname)
+        if parent.proc["filename_cluid"]:
+            Usv, Vsv, xy = None, None, None
+            X = load_spike_times(parent.fname, parent.fname_cluid, parent.st_bin)
+        else:
+            X, Usv, Vsv, xy = load_activity(parent.fname)
         _load_activity_gui(parent, X, Usv, Vsv, xy)
 
     except Exception as e:

rastermap/gui/menus.py

@@ -15,26 +15,32 @@ def mainmenu(parent):
 
     file_menu = main_menu.addMenu("&File")
 
-    loadMat = QAction("&Load data matrix", parent)
+    loadMat = QAction("&Load data matrix (neurons by time)", parent)
     loadMat.setShortcut("Ctrl+L")
     loadMat.triggered.connect(lambda: io.load_mat(parent, name=None))
     parent.addAction(loadMat)
     file_menu.addAction(loadMat)
 
-    parent.loadXY = QAction("&Load xy(z) positions of neurons", parent)
+    loadSt = QAction("Load spike_times and spike_&Clusters", parent)
+    loadSt.setShortcut("Ctrl+C")
+    loadSt.triggered.connect(lambda: io.load_st_clu(parent, name=None))
+    parent.addAction(loadSt)
+    file_menu.addAction(loadSt)
+
+    parent.loadXY = QAction("Load &XY(z) positions of neurons", parent)
     parent.loadXY.setShortcut("Ctrl+X")
     parent.loadXY.triggered.connect(lambda: io.load_neuron_pos(parent))
     parent.addAction(parent.loadXY)
     file_menu.addAction(parent.loadXY)
 
     # load Z-stack
-    parent.loadProc = QAction("&Load z-stack (mean images)", parent)
+    parent.loadProc = QAction("Load &Z-stack (mean images)", parent)
     parent.loadProc.setShortcut("Ctrl+Z")
     parent.loadProc.triggered.connect(lambda: io.load_zstack(parent, name=None))
     parent.addAction(parent.loadProc)
     file_menu.addAction(parent.loadProc)
 
-    parent.loadNd = QAction("Load &n-d variable (times or cont.)", parent)
+    parent.loadNd = QAction("Load &N-d variable (times or cont.)", parent)
     parent.loadNd.setShortcut("Ctrl+N")
     parent.loadNd.triggered.connect(lambda: io.get_behav_data(parent))
     parent.loadNd.setEnabled(False)

rastermap/gui/run.py

@@ -82,7 +82,10 @@ def run_RMAP(self, parent):
         ops_path = os.path.join(os.getcwd(), "rmap_ops.npy")
         np.save(ops_path, self.ops)
         print("Running rastermap with command:")
-        cmd = f"-u -W ignore -m rastermap --ops {ops_path} --S {parent.fname}"
+        if parent.from_spike_times:
+            cmd = f"-u -W ignore -m rastermap --ops {ops_path} --spike_times {parent.fname} --spike_clusters {parent.fname_cluid} --st_bin {parent.st_bin}"
+        else:
+            cmd = f"-u -W ignore -m rastermap --ops {ops_path} --S {parent.fname}"
         if parent.file_iscell is not None:
             cmd += f" --iscell {parent.file_iscell}"
         print("python " + cmd)

rastermap/io.py

@@ -5,6 +5,7 @@
 import numpy as np
 import scipy.io as sio
 from scipy.stats import zscore
+from scipy.sparse import csr_array
 
 def _load_dict(dat, keys):
     X, Usv, Vsv, xpos, ypos, xy = None, None, None, None, None, None
@@ -156,6 +157,16 @@ def load_activity(filename):
 
     return X, Usv, Vsv, xy
 
+def load_spike_times(fname, fname_cluid, st_bin=100):
+    print("Loading " + fname)
+    st = np.load(fname).squeeze()
+    clu = np.load(fname_cluid).squeeze()
+    if len(st) != len(clu):
+        raise ValueError("spike times and clusters must have same length")
+    spks = csr_array((np.ones(len(st), "uint8"), 
+                    (clu, np.floor(st / st_bin * 1000).astype("int"))))
+    spks = spks.todense().astype("float32")
+    return spks
 
 def _cell_center(voxel_mask):
     x = np.median(np.array([v[0] for v in voxel_mask]))