From af9d6e519e67bb636093c4e584f66bc35ab53986 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Sat, 27 Jun 2020 17:09:31 +0800
Subject: [PATCH 01/35] Adds args dictionary to psth

---
 DataProcessingTools/psth.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/DataProcessingTools/psth.py b/DataProcessingTools/psth.py
index 77cba4c..0921e33 100644
--- a/DataProcessingTools/psth.py
+++ b/DataProcessingTools/psth.py
@@ -10,6 +10,7 @@ class PSTH(DPObject):
     def __init__(self, bins, windowsize=1, spiketimes=None, trialidx=None, triallabels=None,
                  alignto=None, trial_event=None, dirs=None):
         DPObject.__init__(self)
+        self.args = {"bins": bins, "windowsize": windowsize, "alignto": alignto}
         tmin = bins[0]
         tmax = bins[-1]
         if spiketimes is None:

From 324bf4e03ac6963eb23fd4a9fd4d0f7647bbb50a Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Sat, 27 Jun 2020 23:58:37 +0800
Subject: [PATCH 02/35] Adds code loading and saving PSTH objects

---
 DataProcessingTools/psth.py | 71 +++++++++++++++++++++++++++++++++++--
 1 file changed, 69 insertions(+), 2 deletions(-)

diff --git a/DataProcessingTools/psth.py b/DataProcessingTools/psth.py
index 0921e33..5499420 100644
--- a/DataProcessingTools/psth.py
+++ b/DataProcessingTools/psth.py
@@ -4,13 +4,38 @@
 from . import levels
 from .raster import Raster
 import os
+import glob
+import h5py
+import hashlib
 
 
 class PSTH(DPObject):
+    filename = "psth.mat"
+
     def __init__(self, bins, windowsize=1, spiketimes=None, trialidx=None, triallabels=None,
-                 alignto=None, trial_event=None, dirs=None):
+                 alignto=None, trial_event=None, dirs=None, redolevel=0, savelevel=1):
         DPObject.__init__(self)
-        self.args = {"bins": bins, "windowsize": windowsize, "alignto": alignto}
+        self.args = {"bins": bins, "windowsize": windowsize,
+                     "alignto": alignto}
+        fname = self.get_filename()
+        if redolevel == 0 and os.path.isfile(fname):
+            self.load(fname)
+        else:
+            # create object
+            self.create(bins, windowsize, spiketimes, trialidx, triallabels,
+                        alignto, trial_event, dirs, savelevel)
+
+    def get_filename(self):
+        """
+        Return the base filename with an argument hash
+        appended
+        """
+        h = self.hash()
+        fname = self.filename.replace(".mat", "_{0}.mat".format(h))
+        return fname
+
+    def create(self, bins, windowsize=1, spiketimes=None, trialidx=None, triallabels=None,
+                      alignto=None, trial_event=None, dirs=None, savelevel=1):
         tmin = bins[0]
         tmax = bins[-1]
         if spiketimes is None:
@@ -58,6 +83,48 @@ def __init__(self, bins, windowsize=1, spiketimes=None, trialidx=None, triallabe
             self.dirs = dirs
         else:
             self.dirs = [os.getcwd()]
+        
+        if savelevel > 0:
+            self.save()
+
+    def load(self, fname=None):
+        if fname is None:
+            fname = self.filename
+        with h5py.File(fname) as ff:
+            args = {}
+            for (k,v) in ff["args"].items():
+                self.args[k] = v
+            self.data = ff["counts"][:]
+            self.ntrials = self.data.shape[0]
+            self.bins = self.args["bins"][:self.data.shape[-1]]
+            self.trial_labels = ff["trial_labels"][:]
+            self.dirs = [s.decode() for s in ff["dirs"][:]]
+            self.setidx = ff["setidx"][:].tolist()
+
+    def hash(self):
+        """
+        Returns a hash representation of this object's arguments.
+        """
+        h = hashlib.sha1()
+        for (k, v) in self.args.items():
+            x = np.atleast_1d(v)
+            h.update(x.tobytes())
+        h.hexdigest()
+
+    def save(self, fname=None):
+        if fname is None:
+            fname = self.get_filename()
+
+        with h5py.File(fname, "w") as ff:
+            args = ff.create_group("args")
+            args["bins"] = self.args["bins"]
+            args["windowsize"] = self.args["windowsize"]
+            if self.args["alignto"] is not None:
+                args["alignto"] = self.args["alignto"]
+            ff["counts"] = self.data
+            ff["trial_labels"] = self.trial_labels
+            ff["dirs"] = np.array(self.dirs, dtype='S256')
+            ff["setidx"] = self.setidx
 
     def append(self, psth):
         if not (self.bins == psth.bins).all():

From ab55da8f0f8a2ed459fe56710321592f62aca580 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Sat, 27 Jun 2020 23:59:02 +0800
Subject: [PATCH 03/35] Updates psth tests

---
 tests/test_psth.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/tests/test_psth.py b/tests/test_psth.py
index 4db38c8..cb34cac 100644
--- a/tests/test_psth.py
+++ b/tests/test_psth.py
@@ -1,6 +1,7 @@
 import numpy as np
 import DataProcessingTools as DPT
 import matplotlib.pylab as plt
+import os
 
 
 def test_psth():
@@ -9,7 +10,10 @@ def test_psth():
     trial_labels = np.random.random_integers(1, 9, (101, ))
     bins = np.arange(0, 100.0, 2.0)
     psth = DPT.psth.PSTH(bins, 1, spiketimes, trialidx, trial_labels,
-                        dirs=["Pancake/20130923/session01/array01/channel001/cell01"])
+                         dirs=["Pancake/20130923/session01/array01/channel001/cell01"],
+                         redolevel=1)
+    # check that something got saved
+    assert os.path.isfile(psth.get_filename())
 
     assert psth.data.shape[0] == 101
 
@@ -27,7 +31,8 @@ def test_psth():
     trialidx = np.random.random_integers(0, 100, (100000, ))
 
     psth2 = DPT.psth.PSTH(bins, 1, spiketimes, trialidx, trial_labels,
-                         dirs= ["Pancake/20130923/session01/array01/channel002/cell01"])
+                          dirs=["Pancake/20130923/session01/array01/channel002/cell01"],
+                          redolevel=1)
     ppsth = DPT.objects.DPObjects([psth])
     ppsth.append(psth2)
     assert ppsth[0] == psth
@@ -63,6 +68,7 @@ def test_sliding_psth():
     trial_labels = np.random.random_integers(1, 9, (101, ))
     bins = np.arange(0, 100.0, 2.0)
     psth = DPT.psth.PSTH(bins, 10, spiketimes, trialidx, trial_labels,
-                        dirs=["Pancake/20130923/session01/array01/channel001/cell01"])
-    assert psth.data.shape == (101, len(bins) - 10)
+                        dirs=["Pancake/20130923/session01/array01/channel001/cell01"],
+                        redolevel=1)
     assert psth.bins.shape == (len(bins) - 10, )
+    assert psth.data.shape == (101, len(bins) - 10)

From 65df1f1d0b67d211f648fd711ab8edcf6b3d6d2d Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Sat, 27 Jun 2020 23:59:16 +0800
Subject: [PATCH 04/35] Updates chain tests

---
 tests/test_chain.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/test_chain.py b/tests/test_chain.py
index cf7a9df..1771601 100644
--- a/tests/test_chain.py
+++ b/tests/test_chain.py
@@ -21,10 +21,11 @@ def test_load():
             raster = DPT.raster.Raster(-0.1, 0.5, trial_events)
             assert (raster.trialidx == [0, 0, 0, 0, 0, 1, 1, 1, 1]).all()
             assert np.isclose(raster.spiketimes, [0.0, 0.05, 0.2, 0.3, 0.4, 0.0, 0.1, 0.2, 0.3]).all()
-            psth = DPT.psth.PSTH([-0.1, 0.2, 0.4, 0.6], alignto=trial_events)
+            psth = DPT.psth.PSTH([-0.1, 0.2, 0.4, 0.6], alignto=trial_events,redolevel=1)
             assert psth.data.shape == (2, 4)
             assert (psth.data[0, :] == [0, 3, 2, 1]).all()
             assert (psth.data[1, :] == [0, 3, 1, 0]).all()
+            os.remove(psth.get_filename())
 
         os.remove(os.path.join(pth, "unit.mat"))
         os.rmdir("Pancake/20130923/session01/array01/channel001/cell01")

From 724ef6ca15351269b0d73e04c093660b6c0125f6 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Sun, 28 Jun 2020 00:08:33 +0800
Subject: [PATCH 05/35] Adds h5py to requirements

---
 requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements.txt b/requirements.txt
index f23634b..830b4c8 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,4 @@
 numpy
 scipy
 matplotlib
+h5py

From 790ef355ab966d0c166e23db5549986c6c6ad197 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Sun, 28 Jun 2020 10:46:50 +0800
Subject: [PATCH 06/35] Adds some general load code to base object

---
 DataProcessingTools/objects.py | 20 ++++++++++++++++++++
 DataProcessingTools/psth.py    | 11 +----------
 2 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/DataProcessingTools/objects.py b/DataProcessingTools/objects.py
index af31228..48e37bc 100644
--- a/DataProcessingTools/objects.py
+++ b/DataProcessingTools/objects.py
@@ -1,5 +1,6 @@
 import numpy as np
 from . import levels
+import h5py
 
 
 class DPObject():
@@ -62,6 +63,25 @@ def append(self, obj):
         for d in obj.dirs:
             self.dirs.append(d)
 
+    def get_filename(self):
+        """
+        Return the base filename with an argument hash
+        appended
+        """
+        h = self.hash()
+        fname = self.filename.replace(".mat", "_{0}.mat".format(h))
+        return fname
+
+    def hash(self):
+        pass
+
+    def loads(self, fname=None):
+        if fname is None:
+            fname = self.get_filename()
+
+        with h5py.File(fname) as ff:
+            self.dirs = [s.decode() for s in ff["dirs"][:]]
+            self.setidx = ff["setidx"][:].tolist()
 
 class DPObjects():
     def __init__(self, objects):
diff --git a/DataProcessingTools/psth.py b/DataProcessingTools/psth.py
index 5499420..be42cdd 100644
--- a/DataProcessingTools/psth.py
+++ b/DataProcessingTools/psth.py
@@ -25,14 +25,6 @@ def __init__(self, bins, windowsize=1, spiketimes=None, trialidx=None, triallabe
             self.create(bins, windowsize, spiketimes, trialidx, triallabels,
                         alignto, trial_event, dirs, savelevel)
 
-    def get_filename(self):
-        """
-        Return the base filename with an argument hash
-        appended
-        """
-        h = self.hash()
-        fname = self.filename.replace(".mat", "_{0}.mat".format(h))
-        return fname
 
     def create(self, bins, windowsize=1, spiketimes=None, trialidx=None, triallabels=None,
                       alignto=None, trial_event=None, dirs=None, savelevel=1):
@@ -88,6 +80,7 @@ def create(self, bins, windowsize=1, spiketimes=None, trialidx=None, triallabels
             self.save()
 
     def load(self, fname=None):
+        DPObject.load(self)
         if fname is None:
             fname = self.filename
         with h5py.File(fname) as ff:
@@ -98,8 +91,6 @@ def load(self, fname=None):
             self.ntrials = self.data.shape[0]
             self.bins = self.args["bins"][:self.data.shape[-1]]
             self.trial_labels = ff["trial_labels"][:]
-            self.dirs = [s.decode() for s in ff["dirs"][:]]
-            self.setidx = ff["setidx"][:].tolist()
 
     def hash(self):
         """

From 7feb7220958d4b33b6366e615aa781b80b6b20fe Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Mon, 29 Jun 2020 21:41:43 +0800
Subject: [PATCH 07/35] Adds code for processing arguments to DPObject

---
 DataProcessingTools/objects.py | 37 +++++++++++++++--
 tests/test_psth.py             | 74 ----------------------------------
 tests/test_raster.py           | 33 ---------------
 tests/test_trialstructures.py  | 71 --------------------------------
 4 files changed, 34 insertions(+), 181 deletions(-)
 delete mode 100644 tests/test_psth.py
 delete mode 100644 tests/test_raster.py
 delete mode 100644 tests/test_trialstructures.py

diff --git a/DataProcessingTools/objects.py b/DataProcessingTools/objects.py
index 48e37bc..f848cd0 100644
--- a/DataProcessingTools/objects.py
+++ b/DataProcessingTools/objects.py
@@ -1,13 +1,44 @@
 import numpy as np
 from . import levels
 import h5py
+import os
 
 
 class DPObject():
+    argsList = []
+    filename = ""
+
     def __init__(self, *args, **kwargs):
-        self.data = np.ndarray((0, 0))
-        self.dirs = []
+        self.dirs = [os.getcwd()]
         self.setidx = []
+        self.args = {}
+        # process positional arguments
+        # TODO: We need to somehow consume these, ie. remove the processed ones
+        pargs = [p for p in filter(lambda t: not isinstance(t, tuple), type(self).argsList)]
+        qargs = pargs.copy()
+        for (k, v) in zip(pargs, args):
+            self.args[k] = v
+            qargs.remove(k)
+        # run the remaining throgh kwargs
+        for k in qargs:
+            if k in kwargs.keys():
+                self.args[k] = kwargs[k]
+
+        # process keyword arguments
+        kargs = filter(lambda t: isinstance(t, tuple), type(self).argsList)
+        for (k, v) in kargs:
+            self.args[k] = kwargs.get(k, v)
+
+        redoLevel = kwargs.get("redoLevel", 0)
+        fname = self.get_filename()
+        if redoLevel == 0 and os.path.isfile(fname):
+            self.load(fname)
+        else:
+            # create object
+            self.create(*args, **kwargs)
+
+    def create(self, *args, **kwargs):
+        pass
 
     def plot(self, i, fig):
         pass
@@ -75,7 +106,7 @@ def get_filename(self):
     def hash(self):
         pass
 
-    def loads(self, fname=None):
+    def load(self, fname=None):
         if fname is None:
             fname = self.get_filename()
 
diff --git a/tests/test_psth.py b/tests/test_psth.py
deleted file mode 100644
index cb34cac..0000000
--- a/tests/test_psth.py
+++ /dev/null
@@ -1,74 +0,0 @@
-import numpy as np
-import DataProcessingTools as DPT
-import matplotlib.pylab as plt
-import os
-
-
-def test_psth():
-    spiketimes = np.cumsum(np.random.exponential(0.3, 100000))
-    trialidx = np.random.random_integers(0, 100, (100000, ))
-    trial_labels = np.random.random_integers(1, 9, (101, ))
-    bins = np.arange(0, 100.0, 2.0)
-    psth = DPT.psth.PSTH(bins, 1, spiketimes, trialidx, trial_labels,
-                         dirs=["Pancake/20130923/session01/array01/channel001/cell01"],
-                         redolevel=1)
-    # check that something got saved
-    assert os.path.isfile(psth.get_filename())
-
-    assert psth.data.shape[0] == 101
-
-    idx = psth.update_idx(1)
-    assert idx == 1
-
-    idx = psth.update_idx(201)
-    assert idx == 100
-
-    psth.plot()
-    fig = plt.gcf()
-    assert len(fig.axes[0].lines) == 9
-
-    spiketimes = np.cumsum(np.random.exponential(0.3, 100000))
-    trialidx = np.random.random_integers(0, 100, (100000, ))
-
-    psth2 = DPT.psth.PSTH(bins, 1, spiketimes, trialidx, trial_labels,
-                          dirs=["Pancake/20130923/session01/array01/channel002/cell01"],
-                          redolevel=1)
-    ppsth = DPT.objects.DPObjects([psth])
-    ppsth.append(psth2)
-    assert ppsth[0] == psth
-    assert ppsth[1] == psth2
-
-    ppsth.plot(0)
-    fig = plt.gcf()
-    assert len(fig.axes[0].lines) == 9
-    ppsth.plot(1, ax=fig.axes[0])
-    assert len(fig.axes[0].lines) == 9
-
-    ppsth.plot(0, ax=fig.axes[0], overlay=True)
-    assert len(fig.axes[0].lines) == 18
-
-    # test appending objects
-    psth.append(psth2)
-
-    assert psth.data.shape[0] == 202
-    assert psth.trial_labels.shape[0] == 202
-    assert len(psth.setidx) == 202
-
-    idx = psth.getindex("cell")
-    data = psth.data[idx(1), :]
-    assert (data == psth2.data).all()
-
-    idx = psth.getindex("session")
-    data = psth.data[idx(0), :]
-    assert (data == psth.data).all()
-
-def test_sliding_psth():
-    spiketimes = np.cumsum(np.random.exponential(0.3, 100000))
-    trialidx = np.random.random_integers(0, 100, (100000, ))
-    trial_labels = np.random.random_integers(1, 9, (101, ))
-    bins = np.arange(0, 100.0, 2.0)
-    psth = DPT.psth.PSTH(bins, 10, spiketimes, trialidx, trial_labels,
-                        dirs=["Pancake/20130923/session01/array01/channel001/cell01"],
-                        redolevel=1)
-    assert psth.bins.shape == (len(bins) - 10, )
-    assert psth.data.shape == (101, len(bins) - 10)
diff --git a/tests/test_raster.py b/tests/test_raster.py
deleted file mode 100644
index 989f071..0000000
--- a/tests/test_raster.py
+++ /dev/null
@@ -1,33 +0,0 @@
-import DataProcessingTools as DPT
-import numpy as np
-import tempfile
-import os
-import scipy.io as sio
-import matplotlib.pylab as plt
-
-
-def test_basic():
-
-    spiketimes = np.array([0.1, 0.15, 0.3, 0.4, 0.5, 0.6,
-                           1.1, 1.2, 1.3, 1.4, 2.5, 2.6])
-    trial_events = np.array([0.1, 1.1])
-
-    raster = DPT.raster.Raster(-0.1, 0.5, alignto=trial_events, spiketimes=spiketimes,
-                               dirs=["session01/array01/channel001/cell01"])
-    assert (raster.trialidx == [0, 0, 0, 0, 0, 1, 1, 1, 1]).all()
-    assert np.isclose(raster.spiketimes, [0.0, 0.05, 0.2, 0.3, 0.4, 0.0, 0.1, 0.2, 0.3]).all()
-
-    # test plotting
-    fig = plt.figure()
-    ax = fig.add_subplot(111)
-    raster.plot(ax=ax)
-    x, y = ax.lines[0].get_data()
-    assert np.isclose(raster.spiketimes, x).all()
-    assert np.isclose(raster.trialidx, y).all()
-
-    raster.append(DPT.raster.Raster(-0.1, 0.5, alignto=trial_events, spiketimes=spiketimes,
-                                   dirs=["session01/array01/channel002/cell01"]))
-    cell_idx = raster.getindex("cell")
-    for i in range(2):
-        assert np.allclose(raster.spiketimes[cell_idx(i)], [0.0, 0.05, 0.2, 0.3, 0.4, 0.0, 0.1, 0.2, 0.3])
-        assert (raster.trialidx[cell_idx(i)] == [0, 0, 0, 0, 0, 1, 1, 1, 1]).all()
diff --git a/tests/test_trialstructures.py b/tests/test_trialstructures.py
deleted file mode 100644
index bdfa1e8..0000000
--- a/tests/test_trialstructures.py
+++ /dev/null
@@ -1,71 +0,0 @@
-import DataProcessingTools as DPT
-import numpy as np
-import os
-
-def test_basic():
-    events = [("trial_start", 0.1),
-              ("target_on", 0.2),
-              ("target_off", 0.5),
-              ("reward_on", 0.6),
-              ("reward_off", 0.8),
-              ("trial_end", 0.85),
-              ("trial_start", 1.1),
-              ("target_on", 1.2),
-              ("target_off", 1.5),
-              ("failure_on", 1.6),
-              ("failure_off", 1.8),
-              ("trial_end", 1.85)]
-
-    trials = DPT.trialstructures.TrialStructure()
-    trials.events = np.array([event[0] for event in events])
-    trials.timestamps = np.array([event[1] for event in events])
-
-    trial_starts = trials.get_timestamps("trial_start")
-    assert (trial_starts == [0.1, 1.1]).all()
-
-def test_working_memory():
-    testdir = "animal/20130923"
-    with DPT.misc.CWD(os.path.join(os.path.dirname(__file__),testdir)):
-        trials = DPT.trialstructures.WorkingMemoryTrials()
-        assert len(trials.events) == 12746
-        trial_starts, trialidx, stimidx = trials.get_timestamps("trial_start")
-        assert len(trial_starts) == 1733
-        assert np.allclose(trial_starts[:2], [47.7139, 50.11616667])
-
-        stim1_onset, trialidx, stimidx = trials.get_timestamps("stimulus_on_1_*")
-        assert len(stim1_onset) == 1915
-        assert np.allclose(stim1_onset[-5:], 
-                            [9107.5137, 9117.90566667, 9164.79406667, 9254.83466667, 9259.95556667])
-
-        stim1_offset, trialidx, stimidx = trials.get_timestamps("stimulus_off_1_*")
-        assert len(stim1_offset) == len(stim1_onset)
-        reward_on, trialidx, stimidx = trials.get_timestamps("reward_on")
-        assert len(reward_on) == 395
-        assert trials.trialidx[-1] == 1732
-
-        stim1_onset, identity, location = trials.get_stim(0)
-        assert len(stim1_onset) == 1434
-        assert identity.count(1) == 1434
-        assert location.count(0) == 417
-        assert location.count(1) == 274
-        assert location.count(2) == 431
-        assert location.count(3) == 312
-
-        # only correct trials
-        reward_onset, ridx, _ = trials.get_timestamps("reward_on")
-        stim1_onset, identity, location = trials.get_stim(0, ridx)
-        assert len(stim1_onset) == 395
-
-    testdir = "animal/20130923/session01"
-    with DPT.misc.CWD(os.path.join(os.path.dirname(__file__),testdir)):
-        trials = DPT.trialstructures.WorkingMemoryTrials()
-        trial_starts,trialidx, stimidx = trials.get_timestamps("trial_start")
-        assert len(trial_starts) == 50
-        assert trial_starts[0] == 0.003666666666667595
-
-
-def test_auto_discovery():
-    testdir = "animal/20130923/session01/array01/channel001/cell01"
-    with DPT.misc.CWD(os.path.join(os.path.dirname(__file__), testdir)):
-        trials = DPT.trialstructures.get_trials()
-        assert len(trials.events) == 12746
\ No newline at end of file

From c592e50c28b8f522779f479b33de2efa22219c61 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Mon, 29 Jun 2020 21:42:22 +0800
Subject: [PATCH 08/35] Updates Spiketrain class with new argument handling

---
 DataProcessingTools/spiketrain.py | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/DataProcessingTools/spiketrain.py b/DataProcessingTools/spiketrain.py
index 170d0dd..e2d2137 100644
--- a/DataProcessingTools/spiketrain.py
+++ b/DataProcessingTools/spiketrain.py
@@ -5,14 +5,22 @@
 
 
 class Spiketrain(DPObject):
-    def __init__(self):
-        DPObject.__init__(self)
-        self.level = "cell"
-        self.filename = "unit.mat"
+    """
+    Spiketrain()
+    """
+    level = "cell"
+    filename = "unit.mat"
+
+    def __init__(self, *args, **kwargs):
+        DPObject.__init__(self, *args, **kwargs)
+        # always load since we do not create spike trains here.
         if os.path.isfile(self.filename):
             self.load()
 
-    def load(self):
+    def load(self, fname=None):
         q = sio.loadmat(self.filename)
         self.timestamps = q["timestamps"]
         self.spikeshape = q["spikeForm"]
+
+    def get_filename(self):
+        return self.filename

From fc48ecdeb789651a661f7be6cf3b3c5f62ad372a Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Mon, 29 Jun 2020 21:42:55 +0800
Subject: [PATCH 09/35] Updates Raster object for new argument handling

---
 DataProcessingTools/raster.py | 50 ++++++++++++++++++++++-------------
 1 file changed, 32 insertions(+), 18 deletions(-)

diff --git a/DataProcessingTools/raster.py b/DataProcessingTools/raster.py
index 4262a0f..4008c92 100644
--- a/DataProcessingTools/raster.py
+++ b/DataProcessingTools/raster.py
@@ -7,32 +7,46 @@
 
 
 class Raster(DPObject):
-    def __init__(self, tmin, tmax, alignto=None, trial_event=None,
-                 spiketimes=None,
-                 trial_labels=None, dirs=None):
-        DPObject.__init__(self)
-        if spiketimes is None:
-            spiketrain = Spiketrain()
-            spiketimes = spiketrain.timestamps.flatten()
-        if alignto is None:
-            trials = get_trials()
-            # convert from seconds to ms
-            alignto = 1000*trials.get_timestamps(trial_event)
-        if trial_labels is None:
-            trial_labels = np.arange(len(alignto))
+    """
+    Raster(tmin, tmax, TrialEvent,trialType, sortBy)
+    """
+    filename = "raster.mat"
+    argsList = ["tmin", "tmax", "trialEvent", "trialType", "sortBy"]
 
+    def __init__(self, *args, **kwargs):
+        DPObject.__init__(self, *args, **kwargs)
+
+    def create(self, *args, **kwargs):
+        trials = get_trials()
+        #TODO: This only works with correct trials for now
+        rewardOnset, cidx, stimIdx = trials.get_timestamps("reward_on")
+        trialEvent = self.args["trialEvent"]
+        alignto, sidx, stimIdx = trials.get_timestamps(trialEvent)
+        qidx = np.isin(sidx, cidx)
+        trialIdx = sidx[qidx]
+        alignto = 1000*alignto[qidx]
+        sortBy = self.args["sortBy"]
+        if sortBy == "stimulus1":
+            stimnr = 0
+        elif sortBy == "stimulus2":
+            stimnr = 1
+        else:
+            ValueError("Unkonwn trial sorting {0}".format(sortBy))
+
+        ts, identity, trialLabel = trials.get_stim(stimnr, trialIdx)
+        #TODO: Never reload spike trains
+        spiketrain = Spiketrain(*args, **kwargs)
+        spiketimes = spiketrain.timestamps
+        tmin = self.args["tmin"]
+        tmax = self.args["tmax"]
         bidx = np.digitize(spiketimes, alignto+tmin)
         idx = (bidx > 0) & (bidx <= np.size(alignto))
         raster = spiketimes[idx] - alignto[bidx[idx]-1]
         ridx = (raster > tmin) & (raster < tmax)
         self.spiketimes = raster[ridx]
         self.trialidx = bidx[idx][ridx]-1
-        self.trial_labels = trial_labels
+        self.trialLabels = trialLabel
         self.setidx = [0 for i in range(len(self.trialidx))]
-        if dirs is None:
-            self.dirs = [os.getcwd()]
-        else:
-            self.dirs = dirs
 
     def append(self, raster):
         DPObject.append(self, raster)

From 7c49f0b16a9b166f4c9597672c14a3efadf06eca Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Mon, 29 Jun 2020 21:43:09 +0800
Subject: [PATCH 10/35] Fixes variable name

---
 DataProcessingTools/raster.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DataProcessingTools/raster.py b/DataProcessingTools/raster.py
index 4008c92..e343ed7 100644
--- a/DataProcessingTools/raster.py
+++ b/DataProcessingTools/raster.py
@@ -57,7 +57,7 @@ def append(self, raster):
         self.trialidx.resize(n_new)
         self.trialidx[n_old:n_new] = raster.trialidx
 
-        self.trial_labels = np.concatenate((self.trial_labels, raster.trial_labels))
+        self.trialLabels = np.concatenate((self.trialLabels, raster.trialLabels))
 
     def plot(self, idx=None, ax=None, overlay=False):
         if ax is None:

From 3d1e7d496e9d0155788af29738fd97b9f575342f Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Mon, 29 Jun 2020 21:44:02 +0800
Subject: [PATCH 11/35] Updates PSTH class with new argument handler

---
 DataProcessingTools/psth.py | 79 ++++++++++++++-----------------------
 1 file changed, 29 insertions(+), 50 deletions(-)

diff --git a/DataProcessingTools/psth.py b/DataProcessingTools/psth.py
index be42cdd..ca5b957 100644
--- a/DataProcessingTools/psth.py
+++ b/DataProcessingTools/psth.py
@@ -10,32 +10,28 @@
 
 
 class PSTH(DPObject):
+    """
+    PSTH(bins,windowSize=1, dirs=None, redoLevel=0, saveLevel=1)
+    """
     filename = "psth.mat"
+    argsList = ["bins", ("windowSize", 1)]
+
+    def __init__(self, *args, **kwargs):
+        """
+        Return a PSTH object using the specified bins
+        """
+        DPObject.__init__(self, *args, **kwargs)
+
+    def create(self, *args, **kwargs):
+        saveLevel = kwargs.get("saveLevel", 1)
+        bins = self.args["bins"]
+
+        # attempt to load from the current directory
+        raster = Raster(bins[0], bins[-1], **kwargs)
+        spiketimes = raster.spiketimes
+        trialidx = raster.trialidx
+        self.trialLabels = raster.trialLabels
 
-    def __init__(self, bins, windowsize=1, spiketimes=None, trialidx=None, triallabels=None,
-                 alignto=None, trial_event=None, dirs=None, redolevel=0, savelevel=1):
-        DPObject.__init__(self)
-        self.args = {"bins": bins, "windowsize": windowsize,
-                     "alignto": alignto}
-        fname = self.get_filename()
-        if redolevel == 0 and os.path.isfile(fname):
-            self.load(fname)
-        else:
-            # create object
-            self.create(bins, windowsize, spiketimes, trialidx, triallabels,
-                        alignto, trial_event, dirs, savelevel)
-
-
-    def create(self, bins, windowsize=1, spiketimes=None, trialidx=None, triallabels=None,
-                      alignto=None, trial_event=None, dirs=None, savelevel=1):
-        tmin = bins[0]
-        tmax = bins[-1]
-        if spiketimes is None:
-            # attempt to load from the current directory
-            raster = Raster(tmin, tmax, alignto=alignto, trial_event=trial_event)
-            spiketimes = raster.spiketimes
-            trialidx = raster.trialidx
-            triallabels = raster.trial_labels
         ntrials = trialidx.max()+1
         counts = np.zeros((ntrials, np.size(bins)), dtype=np.int)
         for i in range(np.size(spiketimes)):
@@ -43,40 +39,25 @@ def create(self, bins, windowsize=1, spiketimes=None, trialidx=None, triallabels
             if 0 <= jj < np.size(bins):
                 counts[trialidx[i], jj] += 1
 
-        self.windowsize = windowsize
-        if windowsize > 1:
-            scounts = np.zeros((ntrials, len(bins)-windowsize))
+        windowSize = self.args["windowSize"]
+        if windowSize > 1:
+            scounts = np.zeros((ntrials, len(bins)-windowSize))
             for i in range(ntrials):
-                for j in range(len(bins)-windowsize):
-                    scounts[i, j] = counts[i, j:j+windowsize].sum()
+                for j in range(len(bins)-windowSize):
+                    scounts[i, j] = counts[i, j:j+windowSize].sum()
 
             self.data = scounts
-            self.bins = bins[:-windowsize]
+            self.bins = bins[:-windowSize]
         else:
             self.data = counts
             self.bins = bins
 
         self.ntrials = ntrials
-        if triallabels is None:
-            self.trial_labels = np.ones((ntrials,))
-        elif np.size(triallabels) == ntrials:
-            self.trial_labels = triallabels
-        elif np.size(triallabels) == np.size(spiketimes):
-            dd = {}
-            for t, l in zip(trialidx, triallabels):
-                dd[t] = l
-            self.trial_labels = np.array([dd[t] for t in range(ntrials)])
-        else:
-            self.trial_labels = triallabels
 
         # index to keep track of sets, e.g. trials
         self.setidx = [0 for i in range(self.ntrials)]
-        if dirs is not None:
-            self.dirs = dirs
-        else:
-            self.dirs = [os.getcwd()]
         
-        if savelevel > 0:
+        if saveLevel > 0:
             self.save()
 
     def load(self, fname=None):
@@ -109,11 +90,9 @@ def save(self, fname=None):
         with h5py.File(fname, "w") as ff:
             args = ff.create_group("args")
             args["bins"] = self.args["bins"]
-            args["windowsize"] = self.args["windowsize"]
-            if self.args["alignto"] is not None:
-                args["alignto"] = self.args["alignto"]
+            args["windowSize"] = self.args["windowSize"]
             ff["counts"] = self.data
-            ff["trial_labels"] = self.trial_labels
+            ff["trialLabels"] = self.trialLabels
             ff["dirs"] = np.array(self.dirs, dtype='S256')
             ff["setidx"] = self.setidx
 

From 3704c1fe2874c0daf192755bf5257fd5bb23d1ca Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Mon, 29 Jun 2020 21:44:36 +0800
Subject: [PATCH 12/35] Adds test for simple object

---
 tests/test_objects.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/tests/test_objects.py b/tests/test_objects.py
index dc3e5d2..06f03f6 100644
--- a/tests/test_objects.py
+++ b/tests/test_objects.py
@@ -48,3 +48,16 @@ def test_append():
 
     idx = obj1.getindex(None)
     assert idx(0) is None
+
+
+def test_object():
+
+    class MyObj(DPT.objects.DPObject):
+        argsList = ["tmin", "tmax"]
+        filename = "test.mat"
+
+    obj = MyObj(-0.1, 1.0)
+
+    assert obj.args["tmin"] == -0.1
+    assert obj.args["tmax"] == 1.0
+    

From 506ff274db2dc1648958072c88f659aab687dced Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Mon, 29 Jun 2020 21:45:03 +0800
Subject: [PATCH 13/35] Changes to hashing code

---
 DataProcessingTools/psth.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/DataProcessingTools/psth.py b/DataProcessingTools/psth.py
index ca5b957..625a9ca 100644
--- a/DataProcessingTools/psth.py
+++ b/DataProcessingTools/psth.py
@@ -77,11 +77,12 @@ def hash(self):
         """
         Returns a hash representation of this object's arguments.
         """
-        h = hashlib.sha1()
+        #TODO: This is not replicable across sessions
+        h = hashlib.sha1(b"psth")
         for (k, v) in self.args.items():
             x = np.atleast_1d(v)
             h.update(x.tobytes())
-        h.hexdigest()
+        return h.hexdigest()
 
     def save(self, fname=None):
         if fname is None:

From d80bd5f8dbc4e7f8a71cd184669268406b07ae1f Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Mon, 29 Jun 2020 21:45:39 +0800
Subject: [PATCH 14/35] Updates WorkingMemoryTrials

---
 DataProcessingTools/trialstructures.py | 67 +++++++++++++++-----------
 1 file changed, 38 insertions(+), 29 deletions(-)

diff --git a/DataProcessingTools/trialstructures.py b/DataProcessingTools/trialstructures.py
index b86f642..611e047 100644
--- a/DataProcessingTools/trialstructures.py
+++ b/DataProcessingTools/trialstructures.py
@@ -8,10 +8,10 @@
 
 
 class TrialStructure(DPObject):
-    def __init__(self):
-        DPObject.__init__(self)
+    def __init__(self, **kwargs):
         self.events = []
         self.timestamps = []
+        DPObject.__init__(self, **kwargs)
 
     def get_timestamps(self, event_label):
         """
@@ -25,34 +25,38 @@ def get_timestamps(self, event_label):
 class WorkingMemoryTrials(TrialStructure):
     filename = "event_markers.csv"
     level = "day"
-    def __init__(self):
-        TrialStructure.__init__(self)
-        self.trialevents = {"session_start": "11000000",
-                            "trial_start": "00000000",
-                            "fix_start": "00000001",
-                            "stimBlankStart": "00000011",
-                            "delay_start": "00000100",
-                            "response_on": "00000101",
-                            "reward_on": "00000110",
-                            "failure": "00000111",
-                            "trial_end": "00100000",
-                            "manual_reward_on": "00001000",
-                            "stim_start": "00001111",
-                            "reward_off ": "00000100",
-                            "trial_start": "00000010",
-                            "target_on": "10100000",
-                            "target_off": "10000000",
-                            "left_fixation": "00011101"}
-        self.reverse_map = dict((v,k) for k,v in self.trialevents.items())
-        self.load()
-
-    def load(self):
+    trialevents = {"session_start": "11000000",
+                   "fix_start": "00000001",
+                   "stimBlankStart": "00000011",
+                   "delay_start": "00000100",
+                   "response_on": "00000101",
+                   "reward_on": "00000110",
+                   "failure": "00000111",
+                   "trial_end": "00100000",
+                   "manual_reward_on": "00001000",
+                   "stim_start": "00001111",
+                   "reward_off": "00000100",
+                   "trial_start": "00000010",
+                   "target_on": "10100000",
+                   "target_off": "10000000",
+                   "left_fixation": "00011101"}
+
+    def __init__(self, **kwargs):
+        self.reverse_map = dict((v, k) for k, v in self.trialevents.items())
+        TrialStructure.__init__(self, **kwargs)
+        # always load
+        if os.path.isfile(self.filename):
+            self.load()
+
+    def load(self, fname=None):
         sessiondir = get_level_name("session")
         leveldir = resolve_level(self.level)
         tidx = -1
         stidx = -1
         self.trialidx = []
         self.stimidx = []
+        self.events = []
+        self.timestamps = []
         with open(os.path.join(leveldir, self.filename), "r") as csvfile:
             data = csv.DictReader(csvfile)
             for row in data:
@@ -113,14 +117,19 @@ def get_timestamps(self, event_label):
         trials.get_timestamps("stimulus_on_1_*")
 
         """
-        idx = np.zeros((len(self.events), ), dtype=np.bool)
+        events = self.events
+        trialidx = self.trialidx
+        timestamps = self.timestamps
+        stimidx = self.stimidx
+
+        idx = np.zeros((len(events), ), dtype=np.bool)
         p = re.compile(event_label)
-        for (i,ee) in enumerate(self.events):
+        for (i ,ee) in enumerate(events):
             m = p.match(ee)
-            if m is not None: 
+            if m is not None:
                 idx[i] = True
-        
-        return self.timestamps[idx], self.trialidx[idx], self.stimidx[idx]
+
+        return timestamps[idx], trialidx[idx], stimidx[idx]
 
     def get_stim(self, stimidx=0, trialidx=None):
         """

From 0dc90de9e6b5a2dd690398cdb52901be02fe6d46 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Mon, 29 Jun 2020 21:46:08 +0800
Subject: [PATCH 15/35] Fixes test_chain

---
 tests/test_chain.py | 51 ++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 43 insertions(+), 8 deletions(-)

diff --git a/tests/test_chain.py b/tests/test_chain.py
index 1771601..e512de3 100644
--- a/tests/test_chain.py
+++ b/tests/test_chain.py
@@ -1,27 +1,62 @@
 import DataProcessingTools as DPT
+from DataProcessingTools.trialstructures import WorkingMemoryTrials
 import tempfile
 import os
 import numpy as np
 import scipy.io as sio
+import csv
 
 
 def test_load():
-    spiketimes = np.array([0.1, 0.15, 0.3, 0.4, 0.5, 0.6,
-                           1.1, 1.2, 1.3, 1.4, 2.5, 2.6])
-    trial_events = np.array([0.1, 1.1])
+    spiketimes = 1000*np.array([0.1, 0.15, 0.3, 0.4, 0.5, 0.6,
+                                1.1, 1.2, 1.3, 1.4, 2.5, 2.6])
+    trialEvents = [("11000001", 0.0),
+                   (WorkingMemoryTrials.trialevents["trial_start"], 0.05),
+                   ("10100001", 0.1),
+                   ("10000001", 0.2),
+                   (WorkingMemoryTrials.trialevents["response_on"], 0.3),
+                   (WorkingMemoryTrials.trialevents["reward_on"], 0.4),
+                   (WorkingMemoryTrials.trialevents["reward_off"], 0.5),
+                   (WorkingMemoryTrials.trialevents["trial_end"], 0.6),
+                   (WorkingMemoryTrials.trialevents["trial_start"], 1.0),
+                   ("10100001", 1.1),
+                   ("10000001", 1.2),
+                   (WorkingMemoryTrials.trialevents["response_on"], 1.3),
+                   (WorkingMemoryTrials.trialevents["reward_on"], 1.4),
+                   (WorkingMemoryTrials.trialevents["reward_off"], 1.5),
+                   (WorkingMemoryTrials.trialevents["trial_end"], 1.6)]
 
     tempdir = tempfile.gettempdir()
     with DPT.misc.CWD(tempdir):
         pth = "Pancake/20130923/session01/array01/channel001/cell01"
         if not os.path.isdir(pth):
             os.makedirs(pth)
-        sio.savemat(os.path.join(pth, "unit.mat"), {"timestamps": spiketimes,
-                                                    "spikeForm": [0]})
+            sio.savemat(os.path.join(pth, "unit.mat"), {"timestamps": spiketimes,
+                                                        "spikeForm": [0]})
         with DPT.misc.CWD(pth):
-            raster = DPT.raster.Raster(-0.1, 0.5, trial_events)
+            with DPT.misc.CWD(DPT.levels.resolve_level("day")):
+                    # save trial info
+                    with open("event_markers.csv", "w") as csvfile:
+                        writer = csv.writer(csvfile)
+                        writer.writerow(["words", "timestamps"])
+                        for ee in trialEvents:
+                            writer.writerow(ee)
+                    trials = DPT.trialstructures.get_trials()
+                    assert len(trials.events) == len(trialEvents)
+
+            trials = DPT.trialstructures.get_trials()
+            assert len(trials.events) == len(trialEvents)
+            stim_onset, tidx, sidx = trials.get_timestamps("stimulus_on_1_*")
+            assert (stim_onset == [0.1, 1.1]).all()
+            spiketrain = DPT.spiketrain.Spiketrain()
+            assert np.allclose(spiketrain.timestamps, spiketimes)
+            raster = DPT.raster.Raster(-100.0, 500.0, "stimulus_on_1_*", "reward_on", "stimulus1")
             assert (raster.trialidx == [0, 0, 0, 0, 0, 1, 1, 1, 1]).all()
-            assert np.isclose(raster.spiketimes, [0.0, 0.05, 0.2, 0.3, 0.4, 0.0, 0.1, 0.2, 0.3]).all()
-            psth = DPT.psth.PSTH([-0.1, 0.2, 0.4, 0.6], alignto=trial_events,redolevel=1)
+            assert np.isclose(raster.spiketimes, [0., 50., 200., 300., 400., 0., 100., 200., 300.]).all()
+            psth = DPT.psth.PSTH([-100., 200., 400., 600.], 1, trialEvent="stimulus_on_1_*",
+                                                               sortBy="stimulus1",
+                                                               trialType="reward_on",
+                                                               redoLevel=1)
             assert psth.data.shape == (2, 4)
             assert (psth.data[0, :] == [0, 3, 2, 1]).all()
             assert (psth.data[1, :] == [0, 3, 1, 0]).all()

From a01a71ebef970450b669f2b859edead02a90cef5 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Mon, 29 Jun 2020 21:46:39 +0800
Subject: [PATCH 16/35] Bumps version number

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index d24cda2..6d166a8 100644
--- a/setup.py
+++ b/setup.py
@@ -1,7 +1,7 @@
 from setuptools import setup
 
 setup(name="DataProcessingTools",
-      version="0.6.0",
+      version="0.7.0",
       description="""Tools for processing data with hierarchical organization""",
       url="https://github.com/grero/DataProcessingTools.git",
       author="Roger Herikstad",

From 61819aeefed57cae2443858f4e92bbd713a7b626 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Mon, 29 Jun 2020 22:05:03 +0800
Subject: [PATCH 17/35] Fixes bug in test_object

---
 tests/test_objects.py | 28 +++++++++++++++++-----------
 1 file changed, 17 insertions(+), 11 deletions(-)

diff --git a/tests/test_objects.py b/tests/test_objects.py
index eda3e46..a5a2d83 100644
--- a/tests/test_objects.py
+++ b/tests/test_objects.py
@@ -1,10 +1,17 @@
 import DataProcessingTools as DPT
 
 
+class MyObj(DPT.objects.DPObject):
+    def __init__(self, dirs, *args, **kwargs):
+        DPT.objects.DPObject.__init__(self, *args, **kwargs)
+        self.dirs = dirs
+        for i in range(len(dirs)):
+            self.setidx.extend([i for j in range(3)])
+
+
 def test_level_idx():
-    obj = DPT.DPObject(dirs=["session01/array01/channel01/cell01",
-                             "session01/array01/channel01/cell02"],
-                       setidx=[0, 0, 0, 1, 1, 1])
+    obj = MyObj(dirs=["session01/array01/channel01/cell01",
+                      "session01/array01/channel01/cell02"])
 
     # test cell level
     idx = obj.getindex("cell")
@@ -17,13 +24,12 @@ def test_level_idx():
 
 
 def test_append():
-    obj1 = DPT.objects.DPObject(dirs=["session01/array01/channel001/cell01",
-                                      "session01/array01/channel001/cell02"],
-                                setidx=[0, 0, 0, 1, 1, 1])
 
-    obj2 = DPT.objects.DPObject(dirs=["session01/array02/channel033/cell01",
-                                      "session01/array02/channel034/cell01"],
-                                setidx=[0, 0, 0, 1, 1, 1])
+    obj1 = MyObj(dirs=["session01/array01/channel001/cell01",
+                        "session01/array01/channel001/cell02"])
+
+    obj2 = MyObj(dirs=["session01/array02/channel033/cell01",
+                         "session01/array02/channel034/cell01"])
 
     obj1.append(obj2)
 
@@ -49,11 +55,11 @@ def test_append():
 
 def test_object():
 
-    class MyObj(DPT.objects.DPObject):
+    class MyObj2(DPT.objects.DPObject):
         argsList = ["tmin", "tmax"]
         filename = "test.mat"
 
-    obj = MyObj(-0.1, 1.0)
+    obj = MyObj2(-0.1, 1.0)
 
     assert obj.args["tmin"] == -0.1
     assert obj.args["tmax"] == 1.0

From 8c6024524ccc562f8c17db4a1b072344d45f8b26 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 13:28:13 +0800
Subject: [PATCH 18/35] Always attempt to load trialstructures

---
 DataProcessingTools/trialstructures.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/DataProcessingTools/trialstructures.py b/DataProcessingTools/trialstructures.py
index 611e047..29c8b4c 100644
--- a/DataProcessingTools/trialstructures.py
+++ b/DataProcessingTools/trialstructures.py
@@ -45,8 +45,7 @@ def __init__(self, **kwargs):
         self.reverse_map = dict((v, k) for k, v in self.trialevents.items())
         TrialStructure.__init__(self, **kwargs)
         # always load
-        if os.path.isfile(self.filename):
-            self.load()
+        self.load()
 
     def load(self, fname=None):
         sessiondir = get_level_name("session")

From ae6856343280898d668a7dea079ce0880d12e2b3 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 13:28:29 +0800
Subject: [PATCH 19/35] Fixes a bug where session was not recognized

---
 DataProcessingTools/trialstructures.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/DataProcessingTools/trialstructures.py b/DataProcessingTools/trialstructures.py
index 29c8b4c..61fc9ec 100644
--- a/DataProcessingTools/trialstructures.py
+++ b/DataProcessingTools/trialstructures.py
@@ -159,7 +159,6 @@ def get_trials():
     """
     for Trials in TrialStructure.__subclasses__():
             leveldir = resolve_level(Trials.level)
-            with CWD(leveldir):
-                if os.path.isfile(Trials.filename):
-                    trials = Trials()
-                    return trials
+            if os.path.isfile(os.path.join(leveldir, Trials.filename)):
+                trials = Trials()
+                return trials

From 6cb9e603318bf05806a2c8b7b032cd14a0a2ebc3 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 13:28:44 +0800
Subject: [PATCH 20/35] Fixes raster alignment

---
 DataProcessingTools/raster.py | 36 +++++++++++++++++++++++------------
 1 file changed, 24 insertions(+), 12 deletions(-)

diff --git a/DataProcessingTools/raster.py b/DataProcessingTools/raster.py
index e343ed7..af3cd25 100644
--- a/DataProcessingTools/raster.py
+++ b/DataProcessingTools/raster.py
@@ -21,22 +21,34 @@ def create(self, *args, **kwargs):
         #TODO: This only works with correct trials for now
         rewardOnset, cidx, stimIdx = trials.get_timestamps("reward_on")
         trialEvent = self.args["trialEvent"]
-        alignto, sidx, stimIdx = trials.get_timestamps(trialEvent)
-        qidx = np.isin(sidx, cidx)
-        trialIdx = sidx[qidx]
-        alignto = 1000*alignto[qidx]
-        sortBy = self.args["sortBy"]
-        if sortBy == "stimulus1":
-            stimnr = 0
-        elif sortBy == "stimulus2":
-            stimnr = 1
+        if "stimulus" in trialEvent:
+            if trialEvent == "stimulus1":
+                stimnr = 0
+            elif trialEvent == "stimulus2":
+                stimnr = 1
+            else:
+                stimnr = -1
+                ValueError("Unkonwn trial sorting {0}".format(trialEvent))
+
+            alignto, stimidx, trialLabel = trials.get_stim(stimnr, cidx)
+            alignto = 1000*np.array(alignto)
         else:
-            ValueError("Unkonwn trial sorting {0}".format(sortBy))
+            alignto, sidx, stimIdx = trials.get_timestamps(trialEvent)
+            qidx = np.isin(sidx, cidx)
+            trialIdx = sidx[qidx]
+            alignto = 1000*alignto[qidx]
+            sortBy = self.args["sortBy"]
+            if sortBy == "stimulus1":
+                stimnr = 0
+            elif sortBy == "stimulus2":
+                stimnr = 1
+            else:
+                ValueError("Unkonwn trial sorting {0}".format(sortBy))
 
-        ts, identity, trialLabel = trials.get_stim(stimnr, trialIdx)
+            ts, identity, trialLabel = trials.get_stim(stimnr, trialIdx)
         #TODO: Never reload spike trains
         spiketrain = Spiketrain(*args, **kwargs)
-        spiketimes = spiketrain.timestamps
+        spiketimes = spiketrain.timestamps.flatten()
         tmin = self.args["tmin"]
         tmax = self.args["tmax"]
         bidx = np.digitize(spiketimes, alignto+tmin)

From 1d7caa4a51cfd197555175da55e3cce5b81f6d9d Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 13:29:04 +0800
Subject: [PATCH 21/35] Fixed trialLabel spelling

---
 DataProcessingTools/psth.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/DataProcessingTools/psth.py b/DataProcessingTools/psth.py
index 625a9ca..c9605f4 100644
--- a/DataProcessingTools/psth.py
+++ b/DataProcessingTools/psth.py
@@ -71,7 +71,7 @@ def load(self, fname=None):
             self.data = ff["counts"][:]
             self.ntrials = self.data.shape[0]
             self.bins = self.args["bins"][:self.data.shape[-1]]
-            self.trial_labels = ff["trial_labels"][:]
+            self.trialLabels = ff["trialLabels"][:]
 
     def hash(self):
         """
@@ -103,7 +103,7 @@ def append(self, psth):
 
         DPObject.append(self, psth)
         self.data = np.concatenate((self.data, psth.data), axis=0)
-        self.trial_labels = np.concatenate((self.trial_labels, psth.trial_labels),
+        self.trialLabels = np.concatenate((self.trialLabels, psth.trialLabels),
                                            axis=0)
         self.ntrials = self.ntrials + psth.ntrials
 
@@ -112,13 +112,13 @@ def plot(self, i=None, ax=None, overlay=False):
             ax = gca()
         if not overlay:
             ax.clear()
-        trial_labels = self.trial_labels[i]
+        trialLabels = self.trialLabels[i]
         data = self.data[i, :]
-        labels = np.unique(trial_labels)
+        labels = np.unique(trialLabels)
 
         for li in range(len(labels)):
             label = labels[li]
-            idx = trial_labels == label
+            idx = trialLabels == label
             mu = data[idx, :].mean(0)
             sigma = data[idx, :].std(0)
             ax.plot(self.bins, mu)

From 9115bd5beb6da479754d47b9b0ad3f713bbdb34e Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 13:35:28 +0800
Subject: [PATCH 22/35] Fixes a bug in tests

---
 tests/test_chain.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_chain.py b/tests/test_chain.py
index e512de3..798ba3a 100644
--- a/tests/test_chain.py
+++ b/tests/test_chain.py
@@ -50,10 +50,10 @@ def test_load():
             assert (stim_onset == [0.1, 1.1]).all()
             spiketrain = DPT.spiketrain.Spiketrain()
             assert np.allclose(spiketrain.timestamps, spiketimes)
-            raster = DPT.raster.Raster(-100.0, 500.0, "stimulus_on_1_*", "reward_on", "stimulus1")
+            raster = DPT.raster.Raster(-100.0, 500.0, "stimulus1", "reward_on", "stimulus1")
             assert (raster.trialidx == [0, 0, 0, 0, 0, 1, 1, 1, 1]).all()
             assert np.isclose(raster.spiketimes, [0., 50., 200., 300., 400., 0., 100., 200., 300.]).all()
-            psth = DPT.psth.PSTH([-100., 200., 400., 600.], 1, trialEvent="stimulus_on_1_*",
+            psth = DPT.psth.PSTH([-100., 200., 400., 600.], 1, trialEvent="stimulus1",
                                                                sortBy="stimulus1",
                                                                trialType="reward_on",
                                                                redoLevel=1)

From c07d1598f410d41a5590f0c34b23a7f6c16ea7ed Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 14:06:23 +0800
Subject: [PATCH 23/35] Fixes a bug in resizing for appending rasters

---
 DataProcessingTools/raster.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/DataProcessingTools/raster.py b/DataProcessingTools/raster.py
index af3cd25..68d947c 100644
--- a/DataProcessingTools/raster.py
+++ b/DataProcessingTools/raster.py
@@ -64,9 +64,9 @@ def append(self, raster):
         DPObject.append(self, raster)
         n_old = len(self.spiketimes)
         n_new = n_old + len(raster.spiketimes)
-        self.spiketimes.resize(n_new)
+        self.spiketimes = np.resize(self.spiketimes, n_new)
         self.spiketimes[n_old:n_new] = raster.spiketimes
-        self.trialidx.resize(n_new)
+        self.trialidx = np.resize(self.trialidx, n_new)
         self.trialidx[n_old:n_new] = raster.trialidx
 
         self.trialLabels = np.concatenate((self.trialLabels, raster.trialLabels))

From 242f466bda1ccc61f2e03cfbcc23bf6fbf07e08c Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 14:07:10 +0800
Subject: [PATCH 24/35] Adds code to always convert to np.array

---
 DataProcessingTools/psth.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/DataProcessingTools/psth.py b/DataProcessingTools/psth.py
index c9605f4..4dd39c0 100644
--- a/DataProcessingTools/psth.py
+++ b/DataProcessingTools/psth.py
@@ -47,10 +47,10 @@ def create(self, *args, **kwargs):
                     scounts[i, j] = counts[i, j:j+windowSize].sum()
 
             self.data = scounts
-            self.bins = bins[:-windowSize]
+            self.bins = np.array(bins[:-windowSize])
         else:
             self.data = counts
-            self.bins = bins
+            self.bins = np.array(bins)
 
         self.ntrials = ntrials
 

From ace8e49188c81a6ce4ffb1383f2a35c5fca63917 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 14:07:25 +0800
Subject: [PATCH 25/35] Adds tests for appending

---
 tests/test_chain.py | 55 ++++++++++++++++++++++++++++++---------------
 1 file changed, 37 insertions(+), 18 deletions(-)

diff --git a/tests/test_chain.py b/tests/test_chain.py
index 798ba3a..005f1a7 100644
--- a/tests/test_chain.py
+++ b/tests/test_chain.py
@@ -28,21 +28,23 @@ def test_load():
 
     tempdir = tempfile.gettempdir()
     with DPT.misc.CWD(tempdir):
-        pth = "Pancake/20130923/session01/array01/channel001/cell01"
-        if not os.path.isdir(pth):
-            os.makedirs(pth)
-            sio.savemat(os.path.join(pth, "unit.mat"), {"timestamps": spiketimes,
-                                                        "spikeForm": [0]})
-        with DPT.misc.CWD(pth):
+        pth = "Pancake/20130923/session01/array01/channel001"
+        for cell in ["cell01", "cell02"]:
+            if not os.path.isdir(os.path.join(pth, cell)):
+                os.makedirs(os.path.join(pth, cell))
+            sio.savemat(os.path.join(pth, cell, "unit.mat"), {"timestamps": spiketimes,
+                                                                  "spikeForm": [0.0]})
+        
+        with DPT.misc.CWD(os.path.join(pth, "cell01")):
             with DPT.misc.CWD(DPT.levels.resolve_level("day")):
-                    # save trial info
-                    with open("event_markers.csv", "w") as csvfile:
-                        writer = csv.writer(csvfile)
-                        writer.writerow(["words", "timestamps"])
-                        for ee in trialEvents:
-                            writer.writerow(ee)
-                    trials = DPT.trialstructures.get_trials()
-                    assert len(trials.events) == len(trialEvents)
+                # save trial info
+                with open("event_markers.csv", "w") as csvfile:
+                    writer = csv.writer(csvfile)
+                    writer.writerow(["words", "timestamps"])
+                    for ee in trialEvents:
+                        writer.writerow(ee)
+                trials = DPT.trialstructures.get_trials()
+                assert len(trials.events) == len(trialEvents)
 
             trials = DPT.trialstructures.get_trials()
             assert len(trials.events) == len(trialEvents)
@@ -50,19 +52,36 @@ def test_load():
             assert (stim_onset == [0.1, 1.1]).all()
             spiketrain = DPT.spiketrain.Spiketrain()
             assert np.allclose(spiketrain.timestamps, spiketimes)
-            raster = DPT.raster.Raster(-100.0, 500.0, "stimulus1", "reward_on", "stimulus1")
+            raster = DPT.raster.Raster(-100.0, 500.0, "stimulus1", "reward_on", "stimulus1",
+                                       redoLevel=1, saveLevel=0)
             assert (raster.trialidx == [0, 0, 0, 0, 0, 1, 1, 1, 1]).all()
             assert np.isclose(raster.spiketimes, [0., 50., 200., 300., 400., 0., 100., 200., 300.]).all()
             psth = DPT.psth.PSTH([-100., 200., 400., 600.], 1, trialEvent="stimulus1",
                                                                sortBy="stimulus1",
                                                                trialType="reward_on",
-                                                               redoLevel=1)
+                                                               redoLevel=1, saveLevel=0)
             assert psth.data.shape == (2, 4)
             assert (psth.data[0, :] == [0, 3, 2, 1]).all()
             assert (psth.data[1, :] == [0, 3, 1, 0]).all()
-            os.remove(psth.get_filename())
 
-        os.remove(os.path.join(pth, "unit.mat"))
+        with DPT.misc.CWD(os.path.join(pth, "cell02")):
+            raster2 = DPT.raster.Raster(-100.0, 500.0, "stimulus1", "reward_on", "stimulus1",
+                                        redoLevel=1, saveLevel=0)
+            psth2 = DPT.psth.PSTH([-100., 200., 400., 600.], 1, trialEvent="stimulus1",
+                                                               sortBy="stimulus1",
+                                                               trialType="reward_on",
+                                                               redoLevel=1, saveLevel=0)
+        raster.append(raster2)
+        cellidx = raster.getindex("cell")
+        assert len(cellidx(1)) == len(raster2.setidx)
+
+        psth.append(psth2)
+        cellidx = psth.getindex("cell")
+        assert len(cellidx(1)) == len(psth2.setidx)
+
+        os.remove(os.path.join(pth, "cell01", "unit.mat"))
+        os.remove(os.path.join(pth, "cell02", "unit.mat"))
         os.rmdir("Pancake/20130923/session01/array01/channel001/cell01")
+        os.rmdir("Pancake/20130923/session01/array01/channel001/cell02")
         os.rmdir("Pancake/20130923/session01/array01/channel001")
         os.rmdir("Pancake/20130923/session01/array01")

From d27079d7da165bd4ff1c1541e70fe997eb675874 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 14:23:11 +0800
Subject: [PATCH 26/35] Adds tests for aligning to second stimulus

---
 tests/test_chain.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/tests/test_chain.py b/tests/test_chain.py
index 005f1a7..df5a1fb 100644
--- a/tests/test_chain.py
+++ b/tests/test_chain.py
@@ -14,6 +14,8 @@ def test_load():
                    (WorkingMemoryTrials.trialevents["trial_start"], 0.05),
                    ("10100001", 0.1),
                    ("10000001", 0.2),
+                   ("01100001", 0.1),
+                   ("01000001", 0.2),
                    (WorkingMemoryTrials.trialevents["response_on"], 0.3),
                    (WorkingMemoryTrials.trialevents["reward_on"], 0.4),
                    (WorkingMemoryTrials.trialevents["reward_off"], 0.5),
@@ -21,6 +23,8 @@ def test_load():
                    (WorkingMemoryTrials.trialevents["trial_start"], 1.0),
                    ("10100001", 1.1),
                    ("10000001", 1.2),
+                   ("01100001", 1.1),
+                   ("01000001", 1.2),
                    (WorkingMemoryTrials.trialevents["response_on"], 1.3),
                    (WorkingMemoryTrials.trialevents["reward_on"], 1.4),
                    (WorkingMemoryTrials.trialevents["reward_off"], 1.5),
@@ -56,6 +60,10 @@ def test_load():
                                        redoLevel=1, saveLevel=0)
             assert (raster.trialidx == [0, 0, 0, 0, 0, 1, 1, 1, 1]).all()
             assert np.isclose(raster.spiketimes, [0., 50., 200., 300., 400., 0., 100., 200., 300.]).all()
+            raster2 = DPT.raster.Raster(-100.0, 500.0, "stimulus2", "reward_on", "stimulus2",
+                                       redoLevel=1, saveLevel=0)
+            assert (raster2.trialidx == [0, 0, 0, 0, 0, 1, 1, 1, 1]).all()
+            assert np.isclose(raster2.spiketimes, [0., 50., 200., 300., 400., 0., 100., 200., 300.]).all()
             psth = DPT.psth.PSTH([-100., 200., 400., 600.], 1, trialEvent="stimulus1",
                                                                sortBy="stimulus1",
                                                                trialType="reward_on",

From f02cce826f23798695c84d30d3b0c4b2cad7f47a Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 14:30:29 +0800
Subject: [PATCH 27/35] Adds tests for plots

---
 tests/test_chain.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/tests/test_chain.py b/tests/test_chain.py
index df5a1fb..8395b87 100644
--- a/tests/test_chain.py
+++ b/tests/test_chain.py
@@ -5,6 +5,7 @@
 import numpy as np
 import scipy.io as sio
 import csv
+import matplotlib.pylab as plt
 
 
 def test_load():
@@ -82,11 +83,14 @@ def test_load():
         raster.append(raster2)
         cellidx = raster.getindex("cell")
         assert len(cellidx(1)) == len(raster2.setidx)
-
+        raster.plot(cellidx(0))
+        xy = plt.gca().lines[0].get_data()
+        assert np.allclose(xy[1], raster.trialidx[cellidx(0)])
         psth.append(psth2)
         cellidx = psth.getindex("cell")
         assert len(cellidx(1)) == len(psth2.setidx)
-
+        psth.plot(cellidx(0))
+        assert len(plt.gca().lines) == 1
         os.remove(os.path.join(pth, "cell01", "unit.mat"))
         os.remove(os.path.join(pth, "cell02", "unit.mat"))
         os.rmdir("Pancake/20130923/session01/array01/channel001/cell01")

From af4dbb8f351498fab541b45fc9dd47dc798486f5 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 14:39:59 +0800
Subject: [PATCH 28/35] Adds test for non-stimulus alignment

---
 tests/test_chain.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/test_chain.py b/tests/test_chain.py
index 8395b87..dc9361f 100644
--- a/tests/test_chain.py
+++ b/tests/test_chain.py
@@ -65,6 +65,9 @@ def test_load():
                                        redoLevel=1, saveLevel=0)
             assert (raster2.trialidx == [0, 0, 0, 0, 0, 1, 1, 1, 1]).all()
             assert np.isclose(raster2.spiketimes, [0., 50., 200., 300., 400., 0., 100., 200., 300.]).all()
+            raster3 = DPT.raster.Raster(-100.0, 500.0, "reward_on", "reward_on", "stimulus2",
+                                       redoLevel=1, saveLevel=0)
+            assert (raster3.trialidx == [0, 0, 0, 1]).all()
             psth = DPT.psth.PSTH([-100., 200., 400., 600.], 1, trialEvent="stimulus1",
                                                                sortBy="stimulus1",
                                                                trialType="reward_on",

From f60bfd2b3ab30d4d1ad5e17aa2345a4605315078 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 14:46:17 +0800
Subject: [PATCH 29/35] Fixes a bug in sliding psth counts

---
 DataProcessingTools/psth.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/DataProcessingTools/psth.py b/DataProcessingTools/psth.py
index 4dd39c0..5b3af27 100644
--- a/DataProcessingTools/psth.py
+++ b/DataProcessingTools/psth.py
@@ -41,9 +41,9 @@ def create(self, *args, **kwargs):
 
         windowSize = self.args["windowSize"]
         if windowSize > 1:
-            scounts = np.zeros((ntrials, len(bins)-windowSize))
+            scounts = np.zeros((ntrials, len(bins)-windowSize+1))
             for i in range(ntrials):
-                for j in range(len(bins)-windowSize):
+                for j in range(len(bins)-windowSize+1):
                     scounts[i, j] = counts[i, j:j+windowSize].sum()
 
             self.data = scounts

From b164d1a48650f5ba47cb95cbcca5f7e8ed4913ae Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 14:46:30 +0800
Subject: [PATCH 30/35] Adsd check for sliding psth

---
 tests/test_chain.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/tests/test_chain.py b/tests/test_chain.py
index dc9361f..9a94f69 100644
--- a/tests/test_chain.py
+++ b/tests/test_chain.py
@@ -75,6 +75,12 @@ def test_load():
             assert psth.data.shape == (2, 4)
             assert (psth.data[0, :] == [0, 3, 2, 1]).all()
             assert (psth.data[1, :] == [0, 3, 1, 0]).all()
+            psths = DPT.psth.PSTH([-100., 200., 400., 600.], windowSize=2, trialEvent="stimulus1",
+                                                               sortBy="stimulus1",
+                                                               trialType="reward_on",
+                                                               redoLevel=1, saveLevel=0)
+            assert psths.args["windowSize"] == 2
+            assert psths.data.shape == (2, 3)
 
         with DPT.misc.CWD(os.path.join(pth, "cell02")):
             raster2 = DPT.raster.Raster(-100.0, 500.0, "stimulus1", "reward_on", "stimulus1",

From 234a635ff0ac65bb531910d7a96668b9fe46a6e8 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 14:51:03 +0800
Subject: [PATCH 31/35] Adds test for trial level indexing

---
 tests/test_objects.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/test_objects.py b/tests/test_objects.py
index a5a2d83..ba8bb16 100644
--- a/tests/test_objects.py
+++ b/tests/test_objects.py
@@ -13,6 +13,10 @@ def test_level_idx():
     obj = MyObj(dirs=["session01/array01/channel01/cell01",
                       "session01/array01/channel01/cell02"])
 
+    # test trial
+    idx = obj.getindex("trial")
+    assert idx(0) == [0]
+
     # test cell level
     idx = obj.getindex("cell")
     assert (idx(0) == [0, 1, 2]).all()

From 3cb97eedcab08c0c9c0aa16cb9194253a6ffef77 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 14:55:08 +0800
Subject: [PATCH 32/35] Updates README

---
 README.md | 73 ++++++++-----------------------------------------------
 1 file changed, 10 insertions(+), 63 deletions(-)

diff --git a/README.md b/README.md
index a249c79..adcd832 100644
--- a/README.md
+++ b/README.md
@@ -27,47 +27,8 @@ celldirs = DPT.levels.get_level_dirs("cell", cwd)
 ### Objects
 ```python
 import DataProcessingTools as DPT
-spiketimes = np.cumsum(np.random.exponential(0.3, 100000))
-trialidx = np.random.random_integers(0, 100, (100000, ))
-trial_labels = np.random.random_integers(1, 9, (101, ))
-bins = np.arange(0, 100.0, 2.0)
-psth1 = DPT.psth.PSTH(spiketimes, trialidx, bins, trial_labels)
-psth1.dirs = ["Pancake/20130923/session01/array01/channel001/cell01"]
-
-spiketimes = np.cumsum(np.random.exponential(0.3, 100000))
-trialidx = np.random.random_integers(0, 100, (100000, ))
-psth2 = DPT.psth.PSTH(spiketimes, trialidx, bins, trial_labels)
-psth2.dirs = ["Pancake/20130923/session01/array01/channel002/cell01"]
-
-# Concatenate the two PSTH objects into a list for plotting
-ppsth = DPT.objects.DPObjects([psth1, psth2])
-
-# Plot the first PSTH
-fig = ppsth.plot(0)
-
-# Plot the second PSTH without overlay
-ppsth.plot(1, overlay=False)
-
-# Append psth2 to psth1, creating an object spanning mulitple sets
-psth1.append(psth2)
-
-# To access the data for the first cell in this compound object
-cell_idx = psth1.getindex("cell")
-
-# The above returns a function that gives the index into the object's data
-# corresponding to the cell level.
-
-# To  access the data related to the first cell, we can do this
-cell1_data = psth1.data[cell_idx(0),:]
-
-# If, on the other hand, we want to group the data by session, we could do
-
-session_idx = psth1.getindex("session")
-session1_data = psth1.data[session_idx(0),:]
-
-# For this example, since we only have a single session, we would be looking
-# at all the data.
 ```
+
 ### A complete example
 Here is an example of how to compute raster and psth for a list for a list of
 cells and step through plots of both using PanGUI
@@ -81,25 +42,6 @@ import PanGUI
 # change this to wherever you keep the data hierarchy
 datadir = os.path.expanduser("~/Documents/workingMemory")
 
-# get the trials for one session
-with DPT.misc.CWD(os.path.join(datadir, "Whiskey/20200106/session02")):
-    trials = DPT.trialstructures.WorkingMemoryTrials()
-
-# get response trials
-response_cue, ridx, _ = trials.get_timestamps("response_on")
-
-# get error trials
-failure, eidx, _ = trials.get_timestamps("failure")
-
-#error trials with response cue
-reidx = np.intersect1d(ridx, eidx)
-
-# get stimulus onset of the error trials
-stim_onset, identity, location = trials.get_stim(0, reidx)
-
-#convert from seconds to ms
-stim_onset = 1000*np.array(stim_onset)
-
 # get all the cells for one session
 with DPT.misc.CWD(os.path.join(datadir, "Whiskey/20200106/session02")):
     cells = DPT.levels.get_level_dirs("cell")
@@ -107,13 +49,18 @@ with DPT.misc.CWD(os.path.join(datadir, "Whiskey/20200106/session02")):
 # gather rasters and PSTH for these cells, for the error trials
 bins = np.arange(-300, 1000.0, 10)
 with DPT.misc.CWD(cells[0]):
-        raster = DPT.raster.Raster(-300.0, 1000.0, stim_onset)
-        psth = DPT.psth.PSTH(bins, 10, raster.spiketimes, raster.trialidx, location)
+    raster = DPT.raster.Raster(-300.0, 1000.0, "stimulus1", "reward_on", "stimulus1",
+                               redoLevel=1, saveLevel=0)
+    psth = DPT.psth.PSTH(bins, 10, trialEvent="stimulus1", sortBy="stimulus1", trialType="reward_on",
+                         redoLevel=1, saveLevel=0)
 for cell in cells[1:]:
     with DPT.misc.CWD(cell):
-        praster = DPT.raster.Raster(-300.0, 1000.0, stim_onset)
+        praster = DPT.raster.Raster(-300.0, 1000.0, "stimulus1", "reward_on", "stimulus1",
+                                    redoLevel=1, saveLevel=0)
         raster.append(praster)
-        psth.append(DPT.psth.PSTH(bins, 10, praster.spiketimes, praster.trialidx, location))
+        ppsth = DPT.psth.PSTH(bins, 10, trialEvent="stimulus1", sortBy="stimulus1", trialType="reward_on",
+                              redoLevel=1, saveLevel=0)
+        psth.append(ppsth)
 
 app = PanGUI.create_window([raster, psth], cols=1, indexer="cell")
 ```

From 00f9ccfbe0639c8f80fed2bcea8d4b84c0d0680d Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 15:01:41 +0800
Subject: [PATCH 33/35] Adds simple object example

---
 README.md | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/README.md b/README.md
index adcd832..64531a3 100644
--- a/README.md
+++ b/README.md
@@ -27,6 +27,24 @@ celldirs = DPT.levels.get_level_dirs("cell", cwd)
 ### Objects
 ```python
 import DataProcessingTools as DPT
+
+class DirFiles(DPT.DPObject):
+    """
+    DirFiles(redoLevels=0, SaveLevels=0, objectLevel='Session')
+    """
+    def __init__(self, *args, **kwargs):
+        # initialize fields in parent
+        DPT.DPObject.__init__(self, *args, **kwargs)
+        # check for files or directories in current directory
+        dir_listing = os.listdir()
+        # check number of items
+        dnum = len(dir_listing)
+        # create object if there are some items in this directory
+        if dnum > 0:
+            # update fields in parent
+            self.dirs = os.getcwd()
+            self.dir_list = dir_listing
+            self.setidx = [0 for i in range(dnum)] 
 ```
 
 ### A complete example

From d594b4e86a82cc5121c059daed474d7678902247 Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 23:08:14 +0800
Subject: [PATCH 34/35] Adds tests for saving and loading PSTH

---
 tests/test_chain.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/tests/test_chain.py b/tests/test_chain.py
index 9a94f69..8b726f8 100644
--- a/tests/test_chain.py
+++ b/tests/test_chain.py
@@ -88,7 +88,17 @@ def test_load():
             psth2 = DPT.psth.PSTH([-100., 200., 400., 600.], 1, trialEvent="stimulus1",
                                                                sortBy="stimulus1",
                                                                trialType="reward_on",
-                                                               redoLevel=1, saveLevel=0)
+                                                               redoLevel=1, saveLevel=1)
+
+            psth3 = DPT.psth.PSTH([-100., 200., 400., 600.], 1, trialEvent="stimulus1",
+                                                               sortBy="stimulus1",
+                                                               trialType="reward_on",
+                                                               redoLevel=0, saveLevel=0)
+            os.remove(psth3.get_filename())
+            assert (psth2.data == psth3.data).all()
+            assert (psth2.args["windowSize"] == psth3.args["windowSize"])
+            assert (psth2.args["bins"] == psth3.args["bins"]).all()
+
         raster.append(raster2)
         cellidx = raster.getindex("cell")
         assert len(cellidx(1)) == len(raster2.setidx)

From db8c06ebfc348f51afdc4da6f99e9c339165ddbe Mon Sep 17 00:00:00 2001
From: roger <roger.herikstad@gmail.com>
Date: Tue, 30 Jun 2020 23:09:26 +0800
Subject: [PATCH 35/35] Fixes an issue with reading from hdf5

---
 DataProcessingTools/psth.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/DataProcessingTools/psth.py b/DataProcessingTools/psth.py
index 5b3af27..418ab65 100644
--- a/DataProcessingTools/psth.py
+++ b/DataProcessingTools/psth.py
@@ -66,8 +66,8 @@ def load(self, fname=None):
             fname = self.filename
         with h5py.File(fname) as ff:
             args = {}
-            for (k,v) in ff["args"].items():
-                self.args[k] = v
+            for (k, v) in ff["args"].items():
+                self.args[k] = v.value
             self.data = ff["counts"][:]
             self.ntrials = self.data.shape[0]
             self.bins = self.args["bins"][:self.data.shape[-1]]