Added a few more files to get flowcharts working

configfile.py

@@ -0,0 +1,194 @@
+# -*- coding: utf-8 -*-
+"""
+configfile.py - Human-readable text configuration file library 
+Copyright 2010  Luke Campagnola
+Distributed under MIT/X11 license. See license.txt for more infomation.
+
+Used for reading and writing dictionary objects to a python-like configuration
+file format. Data structures may be nested and contain any data type as long
+as it can be converted to/from a string using repr and eval.
+"""
+
+import re, os, sys
+from collections import OrderedDict
+GLOBAL_PATH = None # so not thread safe.
+import units
+
+class ParseError(Exception):
+    def __init__(self, message, lineNum, line, fileName=None):
+        self.lineNum = lineNum
+        self.line = line
+        #self.message = message
+        self.fileName = fileName
+        Exception.__init__(self, message)
+        
+    def __str__(self):
+        if self.fileName is None:
+            msg = "Error parsing string at line %d:\n" % self.lineNum
+        else:
+            msg = "Error parsing config file '%s' at line %d:\n" % (self.fileName, self.lineNum)
+        msg += "%s\n%s" % (self.line, self.message)
+        return msg
+        #raise Exception()
+        
+
+def writeConfigFile(data, fname):
+    s = genString(data)
+    fd = open(fname, 'w')
+    fd.write(s)
+    fd.close()
+    
+def readConfigFile(fname):
+    #cwd = os.getcwd()
+    global GLOBAL_PATH
+    if GLOBAL_PATH is not None:
+        fname2 = os.path.join(GLOBAL_PATH, fname)
+        if os.path.exists(fname2):
+            fname = fname2
+            
+    GLOBAL_PATH = os.path.dirname(os.path.abspath(fname))
+        
+    try:
+        #os.chdir(newDir)  ## bad.
+        fd = open(fname)
+        s = unicode(fd.read(), 'UTF-8')
+        fd.close()
+        s = s.replace("\r\n", "\n")
+        s = s.replace("\r", "\n")
+        data = parseString(s)[1]
+    except ParseError:
+        sys.exc_info()[1].fileName = fname
+        raise
+    except:
+        print "Error while reading config file %s:"% fname
+        raise
+    #finally:
+        #os.chdir(cwd)
+    return data
+
+def appendConfigFile(data, fname):
+    s = genString(data)
+    fd = open(fname, 'a')
+    fd.write(s)
+    fd.close()
+
+
+def genString(data, indent=''):
+    s = ''
+    for k in data:
+        sk = str(k)
+        if len(sk) == 0:
+            print data
+            raise Exception('blank dict keys not allowed (see data above)')
+        if sk[0] == ' ' or ':' in sk:
+            print data
+            raise Exception('dict keys must not contain ":" or start with spaces [offending key is "%s"]' % sk)
+        if isinstance(data[k], dict):
+            s += indent + sk + ':\n'
+            s += genString(data[k], indent + '    ')
+        else:
+            s += indent + sk + ': ' + repr(data[k]) + '\n'
+    return s
+    
+def parseString(lines, start=0):
+    
+    data = OrderedDict()
+    if isinstance(lines, basestring):
+        lines = lines.split('\n')
+        
+    indent = measureIndent(lines[start])
+    ln = start - 1
+    
+    try:
+        while True:
+            ln += 1
+            #print ln
+            if ln >= len(lines):
+                break
+            
+            l = lines[ln]
+            
+            ## Skip blank lines or lines starting with #
+            if re.match(r'\s*#', l) or not re.search(r'\S', l):
+                continue
+            
+            ## Measure line indentation, make sure it is correct for this level
+            lineInd = measureIndent(l)
+            if lineInd < indent:
+                ln -= 1
+                break
+            if lineInd > indent:
+                #print lineInd, indent
+                raise ParseError('Indentation is incorrect. Expected %d, got %d' % (indent, lineInd), ln+1, l)
+            
+            
+            if ':' not in l:
+                raise ParseError('Missing colon', ln+1, l)
+            
+            (k, p, v) = l.partition(':')
+            k = k.strip()
+            v = v.strip()
+            
+            ## set up local variables to use for eval
+            local = units.allUnits.copy()
+            local['OrderedDict'] = OrderedDict
+            local['readConfigFile'] = readConfigFile
+            if len(k) < 1:
+                raise ParseError('Missing name preceding colon', ln+1, l)
+            if k[0] == '(' and k[-1] == ')':  ## If the key looks like a tuple, try evaluating it.
+                try:
+                    k1 = eval(k, local)
+                    if type(k1) is tuple:
+                        k = k1
+                except:
+                    pass
+            if re.search(r'\S', v) and v[0] != '#':  ## eval the value
+                try:
+                    val = eval(v, local)
+                except:
+                    ex = sys.exc_info()[1]
+                    raise ParseError("Error evaluating expression '%s': [%s: %s]" % (v, ex.__class__.__name__, str(ex)), (ln+1), l)
+            else:
+                if ln+1 >= len(lines) or measureIndent(lines[ln+1]) <= indent:
+                    #print "blank dict"
+                    val = {}
+                else:
+                    #print "Going deeper..", ln+1
+                    (ln, val) = parseString(lines, start=ln+1)
+            data[k] = val
+        #print k, repr(val)
+    except ParseError:
+        raise
+    except:
+        ex = sys.exc_info()[1]
+        raise ParseError("%s: %s" % (ex.__class__.__name__, str(ex)), ln+1, l)
+    #print "Returning shallower..", ln+1
+    return (ln, data)
+    
+def measureIndent(s):
+    n = 0
+    while n < len(s) and s[n] == ' ':
+        n += 1
+    return n
+    
+    
+    
+if __name__ == '__main__':
+    import tempfile
+    fn = tempfile.mktemp()
+    tf = open(fn, 'w')
+    cf = """
+key: 'value'
+key2:
+    key21: 'value'
+    key22: [1,2,3]
+    key23: 234  #comment
+    """
+    tf.write(cf)
+    tf.close()
+    print "=== Test:==="
+    print cf
+    print "============"
+    data = readConfigFile(fn)
+    print data
+    os.remove(fn)

flowchart/Flowchart.py

@@ -14,7 +14,7 @@ from Terminal import Terminal
 from numpy import ndarray
 import library
 from pyqtgraph.debug import printExc
-import configfile
+import pyqtgraph.configfile as configfile
 import pyqtgraph.dockarea as dockarea
 import pyqtgraph as pg
 import FlowchartGraphicsView

flowchart/library/Filters.py

@@ -197,49 +197,4 @@ class HistogramDetrend(CtrlNode):
         return functions.histogramDetrend(data, window=ws, bins=bn)
 
 
-class ExpDeconvolve(CtrlNode):
-    """Exponential deconvolution filter."""
-    nodeName = 'ExpDeconvolve'
-    uiTemplate = [
-        ('tau', 'spin', {'value': 10e-3, 'step': 1, 'minStep': 100e-6, 'dec': True, 'range': [0.0, None], 'suffix': 's', 'siPrefix': True})
-    ]
-    
-    def processData(self, data):
-        tau = self.ctrls['tau'].value()
-        return functions.expDeconvolve(data, tau)
-        #dt = 1
-        #if isinstance(data, MetaArray):
-            #dt = data.xvals(0)[1] - data.xvals(0)[0]
-        #d = data[:-1] + (self.ctrls['tau'].value() / dt) * (data[1:] - data[:-1])
-        #if isinstance(data, MetaArray):
-            #info = data.infoCopy()
-            #if 'values' in info[0]:
-                #info[0]['values'] = info[0]['values'][:-1]
-            #return MetaArray(d, info=info)
-        #else:
-            #return d
-
-class ExpReconvolve(CtrlNode):
-    """Exponential reconvolution filter. Only works with MetaArrays that were previously deconvolved."""
-    nodeName = 'ExpReconvolve'
-    #uiTemplate = [
-        #('tau', 'spin', {'value': 10e-3, 'step': 1, 'minStep': 100e-6, 'dec': True, 'range': [0.0, None], 'suffix': 's', 'siPrefix': True})
-    #]
-    
-    def processData(self, data):
-        return functions.expReconvolve(data)
-
-class Tauiness(CtrlNode):
-    """Sliding-window exponential fit"""
-    nodeName = 'Tauiness'
-    uiTemplate = [
-        ('window', 'intSpin', {'value': 100, 'min': 3, 'max': 1000000}),
-        ('skip', 'intSpin', {'value': 10, 'min': 0, 'max': 10000000})
-    ]
-    
-    def processData(self, data):
-        return functions.tauiness(data, self.ctrls['window'].value(), self.ctrls['skip'].value())
-        
-        
-    
     

flowchart/library/__init__.py

@@ -3,7 +3,7 @@ from collections import OrderedDict
 import os, types
 from pyqtgraph.debug import printExc
 from ..Node import Node
-import reload
+import pyqtgraph.reload as reload
 
 
 NODE_LIST = OrderedDict()  ## maps name:class for all registered Node subclasses

units.py

@@ -0,0 +1,64 @@
+# -*- coding: utf-8 -*-
+## Very simple unit support:
+##  - creates variable names like 'mV' and 'kHz'
+##  - the value assigned to the variable corresponds to the scale prefix
+##    (mV = 0.001)
+##  - the actual units are purely cosmetic for making code clearer:
+##  
+##    x = 20*pA    is identical to    x = 20*1e-12
+
+## No unicode variable names (μ,Ω) allowed until python 3
+
+SI_PREFIXES = 'yzafpnum kMGTPEZY'
+UNITS = 'm,s,g,W,J,V,A,F,T,Hz,Ohm,S,N,C,px,b,B'.split(',')
+allUnits = {}
+
+def addUnit(p, n):
+    g = globals()
+    v = 1000**n
+    for u in UNITS:
+        g[p+u] = v
+        allUnits[p+u] = v
+    
+for p in SI_PREFIXES:
+    if p ==  ' ':
+        p = ''
+        n = 0
+    elif p == 'u':
+        n = -2
+    else:
+        n = SI_PREFIXES.index(p) - 8
+
+    addUnit(p, n)
+
+cm = 0.01
+
+
+
+
+
+
+def evalUnits(unitStr):
+    """
+    Evaluate a unit string into ([numerators,...], [denominators,...])
+    Examples:
+        N m/s^2   =>  ([N, m], [s, s])
+        A*s / V   =>  ([A, s], [V,])
+    """
+    pass
+    
+def formatUnits(units):
+    """
+    Format a unit specification ([numerators,...], [denominators,...])
+    into a string (this is the inverse of evalUnits)
+    """
+    pass
+    
+def simplify(units):
+    """
+    Cancel units that appear in both numerator and denominator, then attempt to replace 
+    groups of units with single units where possible (ie, J/s => W)
+    """
+    pass
+    
+