Copied demo into colab

.gitignore

@@ -0,0 +1,3 @@
+dist
+leechem.egg-info
+

demo.py

@@ -1,20 +1,19 @@
 #!/usr/bin/python3
 
-import em170428
-
+import leechem
 import numpy as np
 import matplotlib.pyplot as plt 
 
 ############ GENERAL PREPARATION #####################################
 # Connect to the tracing database
-db = em170428.sbemdb.SBEMDB()
+db = leechem.sbemdb.SBEMDB()
 
 # Create a mapping object for converting between various forms of neuron ID
-mp = em170428.mapping.Mapping()
+mp = leechem.mapping.Mapping()
 
 ############ VSD/EPHYS EXAMPLE #######################################
 # Load electrophysiology/VSD trial #9 (an example of local bending)
-tr = em170428.trials.Trial(9)
+tr = leechem.trials.Trial(9)
 
 # Extract timing of electrophysiological stimulus
 stm = tr.stimuli()['P_VL']
@@ -44,7 +43,7 @@
 
 ############ VSD/EM EXAMPLE ##########################################
 # Load electrophysiology/VSD trial #6 (an example of fictive swimming)
-tr = em170428.trials.Trial(6)
+tr = leechem.trials.Trial(6)
 
 # Extract timestamps for the VSD recording
 tt = tr.vsd().timestamps()[0]
@@ -155,7 +154,7 @@
 plt.title('Postsynaptic distance along tree for synapses from DI-1(R) onto DE-3(R)')
 
 ########################## RAW EM DATA EXAMPLE #1 ######################
-idb = em170428.sbemimage.ImageDB()
+idb = leechem.sbemimage.ImageDB()
 # A series of 2x-zoom steps into the raw data
 f, ax = plt.subplots(3,3)
 x = 30

em170428/__init__.py → leechem/__init__.py

@@ -3,3 +3,4 @@
 from . import confidence
 from . import trials
 from . import sbemimage
+__version__ = '1.2'

em170428/confidence.py → leechem/confidence.py

@@ -5,6 +5,7 @@
 import errno
 import os
 import re
+from . import webaccess
 
 class Confidence:
     def __init__(self, csvfn=None):
@@ -26,11 +27,8 @@ def __init__(self, csvfn=None):
         self.gmapconf = {}
         self.vsd2tree = {}
 
-        if csvfn is None:
-            here = os.path.dirname(__file__)
-            csvfn = here + '/../data/confidence.csv'
         lines = []
-        with open(csvfn) as f:
+        with webaccess.opentextfile(csvfn, "confidence.csv") as f:
             dl = csv.unix_dialect()
             rdr = csv.reader(f, dl)
             for row in rdr:

em170428/mapping.py → leechem/mapping.py

@@ -4,6 +4,7 @@
 import csv
 import errno
 import os
+from . import webaccess
 
 class Mapping:
     def __init__(self, csvfn=None):
@@ -31,12 +32,9 @@ def __init__(self, csvfn=None):
         self.can2uct = {}
         self.roiid2roi = {}
         self.roi2roiid = {}
-
-        if csvfn is None:
-            here = os.path.dirname(__file__)
-            csvfn = here + '/../data/mapping.csv'
+
         lines = []
-        with open(csvfn) as f:
+        with webaccess.opentextfile(csvfn, "mapping.csv") as f:
             dl = csv.unix_dialect()
             rdr = csv.reader(f, dl)
             for row in rdr:

em170428/runinfo.py → leechem/runinfo.py

@@ -5,6 +5,7 @@
 import math
 import sys
 import os.path
+from . import webaccess
 
 TILESIZE = 512
 IMAGESIZE = TILESIZE * 33
@@ -51,9 +52,7 @@ def __init__(self, ifn=None):
         class, loading the data from the given hdf5 file.
         pp = RUNINFO() loads the data from the 'positionsummary.h5' 
         file in the em170428 directory.'''
-        if ifn is None:
-            here = os.path.dirname(__file__)
-            ifn = here + '/../data/positionsummary.h5'
+        ifn = webaccess.ensurefile(ifn, "positionsummary.h5")
         self.f = h5.File(ifn, 'r')
 
     BLEND = 1024

em170428/sbemdb.py → leechem/sbemdb.py

@@ -4,6 +4,7 @@
 import sqlite3
 import errno
 import os
+from . import webaccess
 
 class LineSegmentGeom:
     def _dif(pa, pb):
@@ -62,12 +63,7 @@ def __init__(self, dbfn=None):
         '''SBEMDB - Pythonic access to SBEMDB
         db = SBEMDB(dbfn) opens the given database file. db = SBEMDB() opens
         the database file in the em170428 directory.'''
-        if dbfn is None:
-            here = os.path.dirname(__file__)
-            dbfn = here + '/../data/170428_pub.sbemdb'
-        if not os.path.isfile(dbfn):
-            raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
-                                    dbfn)
+        dbfn = webaccess.ensurefile(dbfn, "170428_pub.sbemdb")
         self.db = sqlite3.connect(dbfn)
         self.dbfn = dbfn
 

em170428/trials.py → leechem/trials.py

@@ -4,7 +4,7 @@
 import h5py
 import errno
 import os
-import em170428.salpa
+from . import salpa
 import urllib.request
 import io
 
@@ -76,7 +76,7 @@ def trace(self, k, tau=100, poly=None):
             for k in range(poly+1):
                 y -= p[k] * x**(poly-k)
         elif tau is not None:
-            s = em170428.salpa.Salpa(tau=tau)
+            s = salpa.Salpa(tau=tau)
             y = s.apply(y)
         return (y, '%')
 

em170428/uCT.py → leechem/uCT.py

@@ -11,37 +11,38 @@ def __init__(self, h5fn=None):
         uct = UCT(h5fn) opens the given "uCT-somata.h5" file.
         uct = UCT() opens the default file in the em170428 directory.
         '''
-        if h5fn is None:
-            here = os.path.dirname(__file__)
-            h5fn = here + '/../data/uCT-somata.h5'
-            with h5py.File(h5fn, 'r') as h5:
-                self.somapos = h5['somapos']['value'][:] * 2
-                self.exitpoint = h5['dpp']['value'][:]
-                self.lut = h5['dc']['value'][:]
-                self.tails = {}
-                tt = h5['tails']['value']
-                for k in tt.keys():
-                    if k.startswith('_'):
-                        k1= int(k[1:])
-                        t = tt[k]
-                        t = t['value']
-                        if len(t)==3:
-                            self.tails[k1] = t[:]
-                        else:
-                            self.tails[k] = [[],[],[]] 
+        h5fn = webaccess.ensurefile(h5fn, "uCT-somata.h5")
+        with h5py.File(h5fn, 'r') as h5:
+            self.somapos = h5['somapos']['value'][:] * 2
+            self.exitpoint = h5['dpp']['value'][:]
+            self.lut = h5['dc']['value'][:]
+            self.tails = {}
+            tt = h5['tails']['value']
+            for k in tt.keys():
+                if k.startswith('_'):
+                    k1= int(k[1:])
+                    t = tt[k]
+                    t = t['value']
+                    if len(t)==3:
+                        self.tails[k1] = t[:]
+                    else:
+                        self.tails[k] = [[],[],[]]
+
     def somaPosition(self, uctid):
         '''SOMAPOSITION - Position of a soma
         x,y,z = SOMAPOSITION(uctid) returns the position of a soma.
         UCTID must be a UCT ID (for instance, DE3_R is 1; DI1_R is 66).
         X, Y, Z are in UCT pixel coordinates.'''
         return self.somapos[:,uctid-1]
+
     def exitPointPosition(self, uctid):
         '''EXITPOINTPOSITION - Position of a exit point
         x,y,z = EXITPOINTPOSITION(uctid) returns the position of the point
         where the principal neurite of a cell exits the neuropil.
         UCTID must be a UCT ID (for instance, DE3_R is 1; DI1_R is 66).
         X, Y, Z are in UCT pixel coordinates.'''
         return self.exitpoint[:,uctid-1]
+
     def tailPosition(self, uctid):
         '''TAILPOSITION - Position of a tail
         x,y,z = TAILPOSITION(uctid) returns the position of the “tail”

leechem/webaccess.py

@@ -0,0 +1,41 @@
+#!/usr/bin/python3
+
+import urllib.request
+import shutil
+import os
+from contextlib import contextmanager
+import codecs
+
+@contextmanager
+def opentextfile(fn, dflt):
+    if fn is not None:
+        yield open(fn, mode)
+    here = os.path.dirname(__file__)
+    localfn = here + "/../data/" + dflt
+    if os.path.isfile(localfn):
+        yield open(localfn, mode)
+    url = "https://leechem.caltech.edu/170428/pydata/" + dflt
+    try:
+        req = urllib.request.urlopen(url)
+        yield codecs.iterdecode(req, "utf-8")
+    except urllib.request.HTTPError:
+        raise RuntimeError(f"Could not access {url}")
+
+
+def ensurefile(fn, dflt):
+    if fn is not None:
+        return fn
+    here = os.path.dirname(__file__)
+    localfn = here + "/../data/" + dflt
+    if os.path.isfile(localfn):
+        return localfn
+
+    url = "https://leechem.caltech.edu/170428/pydata/" + dflt
+    localfn = "./" + dflt
+    try:
+        with urllib.request.urlopen(url) as response:
+            with open(localfn, 'wb') as fd:
+                shutil.copyfileobj(response, fd)
+    except urllib.request.HTTPError:
+        raise RuntimeError(f"Could not download {url}")
+    return localfn

pypipush.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+python3 setup.py sdist
+twine upload dist/leechem-1.2.tar.gz

setup.py

@@ -0,0 +1,15 @@
+from setuptools import setup, find_packages
+
+from leechem import __version__
+
+setup(
+    name='leechem',
+    version=__version__,
+
+    url='https://github.com/wagenadl/leechem',
+    author='Daniel A. Wagenaar',
+    author_email='[email protected]',
+    packages=find_packages(),
+    install_requires=['numpy']
+    #py_modules=['leechem'],
+)