import running

baseline_analysis.py

@@ -0,0 +1,16 @@
+import datajoint as dj
+from database import Dataset, Repro
+schema = dj.schema("fish_book", locals())
+
+
+def get_baseline_data(cell_id=None, restriction={}):
+    dsets = []
+    if dataset_name:
+        dsets = (Dataset & ("dataset_id like'%s'" % dataset_name) & restriction)
+    else:
+        dsets = (Dataset & restriction)
+
+    if len(dsets) == 0:
+        return None
+    for d in dsets:
+        d

database.py

@@ -172,7 +172,7 @@ class Repro(dj.Manual):
     definition = """
     repro_id : varchar(512)
     run : smallint
-    -> Dataset
+    -> Dataset # this is wrong! should be cell!?! In our case it is the same...
     ----
     repro_name : varchar(512)
     settings : varchar(3000)
@@ -215,7 +215,6 @@ class Stimulus(dj.Manual):
 
 
 def populate_datasets(data_path, update=False):
-    print("Importing dataset %s" % data_path)
     if not os.path.exists(data_path):
         return
     dset_name = os.path.split(data_path)[-1]
@@ -312,13 +311,21 @@ def populate_cells(data_path):
     if isinstance(firing_rate, str):
         firing_rate = float(firing_rate[:-2])
 
-    if "Identifier" not in subject_info.keys() and ("Identifier" in info.keys() and
-                                                    isinstance(info["Identifier"], dict)):
-        subject_id = "unspecified_" + dset_name
+    subj_id = None
+    if "Identifier" in subject_info.keys():
+        if isinstance(subject_info["Identifier"], dict):
+            subj_id = "unspecified_" + dset_name
+        else:
+            subj_id = subject_info["Identifier"]
+    elif "Identifier" in info.keys():
+        if isinstance(info["Identifier"], dict):
+            subj_id = "unspecified_" + dset_name
+        else:
+            subj_id = info["Identifier"]
     else:
-        subject_id = subject_info["Identifier"]
+        subj_id = "unspecified_" + dset_name
     dataset = dict((Dataset & {"dataset_id": dset_name}).fetch1())
-    subject = dict((Subject & {"subject_id": subject_id}).fetch1())
+    subject = dict((Subject & {"subject_id": subj_id}).fetch1())
 
     dataset_id = dataset["dataset_id"]
     cell_id = "-".join(dataset_id.split("-")[:4]) if len(dataset_id) > 4 else dataset_id
@@ -455,7 +462,10 @@ def scan_folder_for_repros(dataset):
                 ut.find_key_recursive(rs, "Duration", path)
             if len(path) > 0 :
                 stim_duration = ut.deep_get(rs, path, None)
-                stim_duration = float(stim_duration[:-2])
+                if "ms" in stim_duration:
+                    stim_duration = float(stim_duration[:stim_duration.index("ms")])
+                else:
+                    stim_duration = float(stim_duration[:stim_duration.index("s")])
             else:
                 stim_duration = 0.0
 
@@ -491,9 +501,10 @@ def drop_tables():
     Subject.drop()
 
 
-def populate(datasets):
-    for d in datasets:
-        if not populate_datasets(d):
+def populate(datasets, update=False):
+    for i, d in enumerate(datasets):
+        print("Importing %i of %i: %s" % (i, len(datasets), d))
+        if not populate_datasets(d, update):
             continue
         populate_subjects(d)
         populate_cells(d)
@@ -508,6 +519,6 @@ if __name__ == "__main__":
     # data_dir = "../high_freq_chirps/data"
     # drop_tables()
 
-    datasets = glob.glob(os.path.join(data_dir, '/data/apteronotus/201*'))
-    populate(datasets)
+    datasets = glob.glob(os.path.join(data_dir, '/data/eigenmannia/201*'))
+    populate(datasets, update=False)
 

util.py

@@ -5,6 +5,7 @@ import re
 import os
 import glob
 import datetime as dt
+import subprocess
 from IPython import embed
 
 
@@ -15,20 +16,28 @@ def read_info_file(file_name):
     @return: dictionary, the stored information.
     """
     root = {}
-    with open(file_name, 'r') as f:
-        lines = f.readlines()
-        for l in lines:
-            if not l.startswith("#"):
-                continue
-            l = l.strip("#").strip()
-            if len(l) == 0:
-                continue
-            if not ": " in l:  # subsection
-                sec = {}
-                root[l[:-1] if l.endswith(":") else l] = sec
-            else:
-                parts = l.split(': ')
-                sec[parts[0].strip()] = parts[1].strip('"').strip()
+
+    try:
+        with open(file_name, 'r') as f:
+            lines = f.readlines()
+    except UnicodeDecodeError:
+        print("Replacing experimenter!!!")
+        command = "sudo sed -i '/Experimenter/c\#       Experimenter: Anna Stoeckl' %s" % file_name
+        subprocess.check_call(command, shell=True)
+        with open(file_name, 'r') as f:
+            lines = f.readlines()
+    for l in lines:
+        if not l.startswith("#"):
+            continue
+        l = l.strip("#").strip()
+        if len(l) == 0:
+            continue
+        if not ": " in l:  # subsection
+            sec = {}
+            root[l[:-1] if l.endswith(":") else l] = sec
+        else:
+            parts = l.split(': ')
+            sec[parts[0].strip()] = parts[1].strip('"').strip()
     return root