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[Pyphant-devel] SF.net SVN: pyphant:[700] trunk/src
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From: <zk...@us...> - 2011-05-23 12:48:46
|
Revision: 700
http://pyphant.svn.sourceforge.net/pyphant/?rev=700&view=rev
Author: zklaus
Date: 2011-05-23 12:48:36 +0000 (Mon, 23 May 2011)
Log Message:
-----------
Merge branch 'master' into svn-trunk
* master: (42 commits)
Enh: Added loadRecipe method to H5FileHandler
Fix: Workaround for Statistics.Histogram
Fix: Worker.py: unwanted sharing of annotations
Fix: KM: removed ProgressDialog if no wx present
Enh: Faster hashing for FieldContainers
Fix: Docstrings in toolboxes
Merge: Autofocus
Fix: Type of name parameter of workers
Bar chart: Increase range from [0:ymax] to [min(ymin,0):ymax]
MRA: - Bugfix: Local Extrema Systematically Shifted
- "OSC.MRA" Bugfix: Removed systematic error in calculation of local extrema
Fix: Dimensions in AlgebraWorker
Revert: Undo last 2 commits
Fix: tried to fix dimensions in AlgebraWorker
Fix: started working on dimensions in AlgebraWorker
Fix: AlgebraWorker: Sealing of DCs
Enh: Added wildcard support to FileButton
Test: Tried working on the FileButton of FMFLoader
Fix: Put workers back into the ImageProcessing toolbox
Fix: Made OscMapper worker independent of OscAbsorption
...
Modified Paths:
--------------
trunk/src/pyphant/pyphant/core/DataContainer.py
trunk/src/pyphant/pyphant/core/FieldContainer.py
trunk/src/pyphant/pyphant/core/H5FileHandler.py
trunk/src/pyphant/pyphant/core/Helpers.py
trunk/src/pyphant/pyphant/core/KnowledgeManager.py
trunk/src/pyphant/pyphant/core/Worker.py
trunk/src/pyphant/pyphant/tests/TestDataContainer.py
trunk/src/pyphant/pyphant/visualizers/Chart.py
trunk/src/pyphant/pyphant/visualizers/ZStackVisualizer.py
trunk/src/pyphant/pyphant/visualizers/__init__.py
trunk/src/pyphant/pyphant/wxgui2/paramvisualization/FileButton.py
trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
trunk/src/workers/ImageProcessing/ImageProcessing/ApplyMask.py
trunk/src/workers/ImageProcessing/ImageProcessing/AutoFocus.py
trunk/src/workers/ImageProcessing/ImageProcessing/BiThresholdingWorker.py
trunk/src/workers/ImageProcessing/ImageProcessing/CoverageWorker.py
trunk/src/workers/ImageProcessing/ImageProcessing/DiffWorker.py
trunk/src/workers/ImageProcessing/ImageProcessing/DistanceMapper.py
trunk/src/workers/ImageProcessing/ImageProcessing/EdgeFillWorker.py
trunk/src/workers/ImageProcessing/ImageProcessing/EdgeTouchingFeatureRemover.py
trunk/src/workers/ImageProcessing/ImageProcessing/EnhanceContrast.py
trunk/src/workers/ImageProcessing/ImageProcessing/FindLocalExtrema.py
trunk/src/workers/ImageProcessing/ImageProcessing/FitBackground.py
trunk/src/workers/ImageProcessing/ImageProcessing/Gradient.py
trunk/src/workers/ImageProcessing/ImageProcessing/ImageLoaderWorker.py
trunk/src/workers/ImageProcessing/ImageProcessing/InvertWorker.py
trunk/src/workers/ImageProcessing/ImageProcessing/Medianiser.py
trunk/src/workers/ImageProcessing/ImageProcessing/NDImageWorker.py
trunk/src/workers/ImageProcessing/ImageProcessing/OptimalContrastWorker.py
trunk/src/workers/ImageProcessing/ImageProcessing/SkeletonizeFeature.py
trunk/src/workers/ImageProcessing/ImageProcessing/ThresholdingWorker.py
trunk/src/workers/ImageProcessing/ImageProcessing/UltimatePointsCalculator.py
trunk/src/workers/ImageProcessing/ImageProcessing/Watershed.py
trunk/src/workers/ImageProcessing/ImageProcessing/__init__.py
trunk/src/workers/ImageProcessing/setup.py
trunk/src/workers/OSC/OSC/ErrorEstimator.py
trunk/src/workers/OSC/OSC/EstimateParameterFromValues.py
trunk/src/workers/OSC/OSC/ExtremumFinder.py
trunk/src/workers/OSC/OSC/OscAbsorption.py
trunk/src/workers/OSC/OSC/__init__.py
trunk/src/workers/OSC/OSC/tests/TestMRA.py
trunk/src/workers/Statistics/Statistics/Histogram.py
trunk/src/workers/Statistics/setup.py
trunk/src/workers/fmfile/fmfile/FMFLoader.py
trunk/src/workers/tools/setup.py
trunk/src/workers/tools/tools/__init__.py
Added Paths:
-----------
trunk/src/workers/ImageProcessing/ImageProcessing/MarkInclusions.py
trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestAutoFocus.py
trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/
trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/
trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z00.tif
trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z01.tif
trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z02.tif
trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z03.tif
trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z04.tif
trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z05.tif
trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z06.tif
trunk/src/workers/OSC/OSC/OscMapper.py
trunk/src/workers/tools/tools/AddColumn.py
trunk/src/workers/tools/tools/AlgebraWorker.py
trunk/src/workers/tools/tools/ColumnExtractor.py
trunk/src/workers/tools/tools/ExtractRows.py
trunk/src/workers/tools/tools/MRA.py
trunk/src/workers/tools/tools/Slicing.py
Removed Paths:
-------------
trunk/src/pyphant/pyphant/core/XMLHandler.py
trunk/src/pyphant/pyphant/core/ZStackManager.py
trunk/src/pyphant/pyphant/tests/TestZStacks.py
trunk/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z00.tif
trunk/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z01.tif
trunk/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z02.tif
trunk/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z03.tif
trunk/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z04.tif
trunk/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z05.tif
trunk/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z06.tif
trunk/src/pyphant/pyphant/tests/resources/zstack/_meta.xml
trunk/src/pyphant/pyphant/tests/resources/zstack/single_meta.xml
trunk/src/pyphant/pyphant/visualizers/SingleValueVisualizer.py
trunk/src/workers/ImageProcessing/ImageProcessing/FeatureRatio.py
trunk/src/workers/ImageProcessing/ImageProcessing/FilterWorker.py
trunk/src/workers/ImageProcessing/ImageProcessing/MarkAF.py
trunk/src/workers/ImageProcessing/ImageProcessing/Reduce.py
trunk/src/workers/ImageProcessing/ImageProcessing/SliceSelector.py
trunk/src/workers/OSC/OSC/AddColumn.py
trunk/src/workers/OSC/OSC/MRA.py
trunk/src/workers/OSC/OSC/Slicing.py
Modified: trunk/src/pyphant/pyphant/core/DataContainer.py
===================================================================
--- trunk/src/pyphant/pyphant/core/DataContainer.py 2010-09-13 08:56:34 UTC (rev 699)
+++ trunk/src/pyphant/pyphant/core/DataContainer.py 2011-05-23 12:48:36 UTC (rev 700)
@@ -36,7 +36,7 @@
=============================================================================
The *DataContainer* is Pypahnt's preferred data exchange class. It is
-designed to maximise the interoperability of the various workers
+designed to maximize the interoperability of the various workers
provided by Pyphant.
It can be seen as an interface for exchanging data between workers and
@@ -58,7 +58,7 @@
=============================================================
The *SampleContainer* combines different FieldContainers that have the
-same numer of sample points to a table-like representation. It stores
+same number of sample points to a table-like representation. It stores
different observations on the same subject per row whereby each column
comprises a quantity of the same kind. Each row can be regarded as the
realization of a random variable.
@@ -71,10 +71,9 @@
import copy, hashlib, threading, numpy, StringIO
import os, platform, datetime, socket, urlparse
-from pyphant.quantities import (isQuantity,
- Quantity)
+from pyphant.quantities import (isQuantity, Quantity)
import Helpers
-
+from ast import (NodeTransformer, NodeVisitor)
import logging
_logger = logging.getLogger("pyphant")
@@ -83,7 +82,7 @@
enc = lambda s: unicode(s, "utf-8")
def parseId(id):
- u"""Returns tupple (HASH, TYPESTRING) from given .id attribute."""
+ u"""Returns tuple (HASH, TYPESTRING) from given .id attribute."""
resUri = urlparse.urlsplit(id)
return resUri[2].split('/')[-1].split('.') #(hash, uriType)
@@ -293,446 +292,152 @@
def numberOfColumns(self):
return len(self.columns)
- def _getCommands(self, expression):
+ def calcColumn(self, exprStr, shortname, longname):
"""
- This method generates nested tuples of filter commands to be applied
- to a SampleContainer out of a string expression. For details of the
- output see SampleContainer.filter()
- expression -- String describing the filter commands. For details
- see SampleContainer.filter(expression)
+ Return an unsealed FieldContainer generated from `exprStr`.
+
+ Parameters
+ ----------
+ exprStr : str
+ Expression has to be a string. Specifies the mathematical
+ operations which will be evaluated to generate a new FieldContainer
+ containing the result. `exprStr` may contain FieldContainers,
+ PhysicalQuantities, Booleans and Numbers as well as the operators
+ listed below.
+
+ shortname : str
+ The `shortname` of the returned FieldContainer.
+
+ longname : str
+ The `longname`of the returned FieldContainer.
+
+ Syntax
+ ------
+ FieldContainer
+ FieldContainers can be adressed by their `shortname`or `longname`.
+ For a FieldContainer with shortname="exampleFC" the syntax within
+ `exprStr` is:
+ col("exampleFC")
+ where `col` stands for column and may be `Col` or `COL` as well.
+ Adressing by `longname` works analogously.
+
+ PhysicalQuantity
+ Within the expression PhysicalQuantities have to be enquoted:
+ "10kg", "100 m", "5 kg * m / s ** 2"
+ where the whitespaces are optional.
+
+ Booleans and Numbers
+ Can just be used without quotes or braces within `exprStr`:
+ True, False, 1.2, 10
+
+ Operators
+ ---------
+ A list of all implemented operations that can be used within `exprStr`
+ sorted by precedence from lowest precedence (least binding) to highest
+ precedence (most binding):
+
+ Comparisons: <, <=, >, >=, <>, !=, ==
+ Bitwise OR: |
+ Bitwise XOR: ^
+ Bitwise AND: &
+ Addition and Subtraction: +, -
+ Multiplication, Division: *, /
+ Positive, Negative, Bitwise NOT: +x, -x, ~x
+
+ Not implemented: and, or, not, **, //, %, if - else
+
+ Examples
+ --------
+ Some examples of valid expressions will be given.
+ Data:
+ distance = FieldContainer(scipy.array([5., 10., 1.]),
+ Quantity('1.0 m'),
+ longname=u"Distance",
+ shortname=u"s")
+ time = FieldContainer(scipy.array([3., 4., 5.]),
+ Quantity('1.0 s'),
+ longname=u"Time",
+ shortname=u"t")
+ Examplary expressions:
+ exprStr = "col('Distance') / col('Time')"
+ exprStr = "col('Distance') - '1 m'"
+ exprStr = "col('t') >= '4 s'"
+ exprStr = "(col('s') > '1 m') & (COL('Time') == '3s')"
+
"""
- #TODO: compare SCColumns with each other,
- # allow multi dimensional columns (think up new syntax)
- import re
- #test for expressions containing whitespaces only:
- if len(re.findall(r'\S', expression)) == 0:
- return ()
- #prepare regular expressions
- reDoubleQuotes = re.compile(r'("[^"][^"]*")')
- reSplit = re.compile(
- r'(<(?!=)|<=|>(?!=)|>=|==|!=|not|NOT|and|AND|or|OR|\(|\))'
- )
- reCompareOp = re.compile(r'<|>|==|!=')
- #split the expression
- DQList = reDoubleQuotes.split(expression)
- splitlist = []
- for dq in DQList:
- if reDoubleQuotes.match(dq) != None: splitlist.append(dq)
- else: splitlist.extend(reSplit.split(dq))
- #identify splitted Elements
- al = [] #<-- abstractlist containing tuples of (type, expression)
- for e in splitlist:
- if len(re.findall(r'\S', e)) == 0: pass #<-- skip whitespaces
- elif reCompareOp.match(e) != None:
- al.append(('CompareOp', e))
- elif reSplit.match(e) != None:
- al.append(('Delimiter', e.lower()))
- elif reDoubleQuotes.match(e) != None:
- column = None
- try:
- column = self[e[1:-1]]
- except:
- raise IndexError(
- 'Could not find column ' + e + ' in "'
- + self.longname + '".'
- )
- al.append(('SCColumn', column))
+ exprStr = exprStr or 'True'
+ import ast
+ rpn = ReplaceName(self)
+ expr = compile(exprStr, "<calcColumn>", 'eval', ast.PyCF_ONLY_AST)
+ replacedExpr = rpn.visit(expr)
+ rpo = ReplaceOperator(rpn.localDict)
+ factorExpr = rpo.visit(replacedExpr)
+ localDict = dict([(key, value.data) \
+ for key, value in rpn.localDict.iteritems()])
+ data = eval(compile(factorExpr, '<calcColumn>', 'eval'), {}, localDict)
+ unitcalc = UnitCalculator(rpn.localDict)
+ unit, dims = unitcalc.getUnitAndDim(replacedExpr)
+ if dims is None:
+ assert not isinstance(data, numpy.ndarray)
+ for col in self.columns:
+ checkDimensions(col.dimensions[0],
+ self.columns[0].dimensions[0])
+ shape = self.columns[0].dimensions[0].data.shape
+ if data:
+ data = numpy.ones(shape, dtype=bool)
else:
- try:
- phq = Quantity(e)
- al.append(('PhysQuant', phq))
- continue
- except:
- try:
- number = Quantity(e+' m')
- al.append(('Number', eval(e)))
- continue
- except: pass
- raise ValueError, "Error parsing expression: " + e
- #resolve multiple CompareOps like a <= b <= c == d:
- i = 0
- values = ['PhysQuant', 'SCColumn', 'Number']
- start_sequence = -1
- while i < len(al) - 4:
- if ((al[i][0] in values) and (al[i+1][0] == 'CompareOp')
- and (al[i+2][0] in values) and (al[i+3][0] == 'CompareOp')
- and (al[i+4][0] in values)):
- if start_sequence == -1:
- start_sequence = i
- al.insert(i+3, ('Delimiter', 'and'))
- al.insert(i+4, al[i+2])
- i += 4
- else:
- #'not' has higher precedence than 'and':
- if start_sequence != -1:
- al.insert(start_sequence, ('Delimiter', '('))
- al.insert(i+4, ('Delimiter', ')'))
- start_sequence = -1
- i += 3
- else:
- i += 1
- if start_sequence != -1:
- al.insert(start_sequence, ('Delimiter', '('))
- al.insert(i+4, ('Delimiter', ')'))
- #identify atomar components like "a" <= 10m, 10s > "b",
- #... and compress them:
- if al[0][0] == 'CompareOp':
- raise ValueError(
- al[0][1] + " may not stand at the beginning of an expression!"
- )
- i = 1
- valid = False
- while i < len(al):
- if al[i][0] == 'CompareOp':
- left = al.pop(i-1)
- middle = al.pop(i-1)
- right = al.pop(i-1)
- if left[0] not in values:
- raise TypeError, str(left[1]) + " is not a proper value."
- if right[0] not in values:
- raise TypeError, str(right[1]) + " is not a proper value."
- al.insert(i-1, ('Atomar', left, middle[1], right))
- valid = True
- i += 1
- if not valid:
- raise ValueError(
- "There has to be at least one valid comparison: " + expression
- )
+ data = numpy.zeros(shape, dtype=bool)
+ dims = [self.columns[0].dimensions[0]]
+ field = FieldContainer(data, unit, dimensions=dims,
+ longname=longname, shortname=shortname)
+ return field
- def compressBraces(sublist):
- """
- Identifies braces and compresses them recursively.
- sublist -- list of filter commands
- """
- openbraces = 0
- start = 0
- end = 0
- finished = False
- for i in range(len(sublist)):
- if sublist[i] == ('Delimiter', '('):
- openbraces += 1
- if openbraces == 1 and not finished:
- start = i
- elif sublist[i] == ('Delimiter', ')'):
- openbraces -= 1
- if openbraces == 0 and not finished:
- end = i
- finished = True
- if openbraces != 0:
- raise ValueError(
- "There are unmatched braces within the expression: "
- + expression
- )
- if start == 0 and end == 0:
- #no more braces found: end of recursion
- return sublist[:]
- else:
- if end-start == 1:
- raise ValueError(
- "There are braces enclosing nothing in the expression: "
- + expression
- )
- middle = None
- if end-start == 2:
- #discard unnecessary braces in order to reduce
- #recursion depth later on:
- middle = sublist[start+1:start+2]
- else:
- middle = [('Brace', compressBraces(sublist[start+1:end]))]
- return sublist[0:start]+middle+compressBraces(sublist[end+1:])
- #TODO: The following three methods could be merged into one generalized
- #method for compressing unitary and binary operators. This would be
- #useful in a future version when there are lots of operators to be
- #supported.
+ def filter(self, exprStr, shortname='', longname=''):
+ """
+ Return an unsealed SampleContainer containing only those rows where
+ `exprStr` was evaluated to be True. This method replaces the old
+ filter method and is mostly capable of the same operations, yet the
+ syntax has changed slightly.
- def compressNot(sublist):
- """
- Identifies "not"s and compresses them recursively.
- sublist -- list of filter commands
- """
- i = 0
- while i < len(sublist):
- if sublist[i] == ('Delimiter', 'not'):
- if i+1 >= len(sublist):
- raise ValueError(
- "'not' must not stand at the end of an expression: "
- + expression
- )
- x = sublist[i+1]
- if x[0] == 'Atomar':
- retlist = sublist[0:i] + [('NOT', x)]
- retlist += compressNot(sublist[i+2:])
- return retlist
- elif x[0] == 'Brace':
- retlist = sublist[0:i]
- retlist += [('NOT', ('Brace', compressNot(x[1])))]
- retlist += compressNot(sublist[i+2:])
- return retlist
- else:
- raise ValueError(
- "'not' cannot be applied to " + str(x) + "."
- )
- elif sublist[i][0] == 'Brace':
- retlist = sublist[0:i]
- retlist += [('Brace', compressNot(sublist[i][1]))]
- retlist += compressNot(sublist[i+1:])
- return retlist
- i += 1
- return sublist[:]
+ Parameters
+ ----------
+ exprStr : str
+ A string with a logical expression that has to evaluate to be
+ either True or False. This can be for example an inequality or
+ a comparison. For all possible operations and a description of
+ the syntax as well as examples see `calcColumn`.
- def compressAnd(sublist, start=0):
- """
- Identifies "and"s and compresses them recursively:
- start -- start == 1 indicates that the 1st element of sublist
- has already been compressed. This is necessary for
- binary operators.
- sublist -- list of filter commands
- """
- i = start
- while i < len(sublist):
- if sublist[i] == ('Delimiter', 'and'):
- left = None
- if start == 1 and i == 1: left = sublist[i-1]
- else: left = compressAnd(sublist[i-1:i])[0]
- if left[0] not in ['NOT', 'AND', 'Brace', 'Atomar']:
- raise ValueError(
- "'and' cannot be applied to " + str(left) + "."
- )
- right = compressAnd(sublist[i+1:i+2])[0]
- if right[0] not in ['NOT', 'AND', 'Brace', 'Atomar']:
- raise ValueError(
- "'and' cannot be applied to " + str(right) + "."
- )
- retlist = sublist[0:i-1]
- retlist += compressAnd([('AND', left, right)]+sublist[i+2:],
- 1)
- return retlist
- elif sublist[i][0] == 'Brace':
- retlist = sublist[0:i]
- retlist += compressAnd([('Brace',
- compressAnd(sublist[i][1]))]
- + sublist[i+1:], 1)
- return retlist
- elif sublist[i][0] == 'NOT':
- retlist = sublist[0:i]
- retlist += compressAnd([('NOT',
- compressAnd([sublist[i][1]])[0])]
- + sublist[i+1:], 1)
- return retlist
- i += 1
- return sublist[:]
+ shortname, longname : str, default=''
+ Specify the short and long name of the resulting FC.
- def compressOrDCB(sublist, start=0):
- """
- Identifies "or"s and compresses them recursively.
- Decompresses braces in order to reduce recursion depth later on.
- start -- start == 1 indicates that the 1st element of sublist
- has already been compressed. This is necessary for
- binary operators.
- sublist -- list of filter commands
- """
- i = start
- while i < len(sublist):
- if sublist[i] == ('Delimiter', 'or'):
- left = None
- if start == 1 and i == 1: left = sublist[i-1]
- else: left = compressOrDCB(sublist[i-1:i])[0]
- if left[0] not in ['NOT', 'AND', 'Atomar', 'OR']:
- raise ValueError(
- "'or' cannot be applied to " + str(left) + "."
- )
- right = compressOrDCB(sublist[i+1:i+2])[0]
- if right[0] not in ['NOT', 'AND', 'Atomar', 'OR']:
- raise ValueError(
- "'or' cannot be applied to " + str(right) + "."
- )
- retlist = sublist[0:i-1]
- retlist += compressOrDCB([('OR', left, right)]
- + sublist[i+2:], 1)
- return retlist
- elif sublist[i][0] == 'Brace':
- inner = compressOrDCB(sublist[i][1])
- if len(inner) != 1:
- raise ValueError(
- "Expression could not be parsed completely."
- "(probably missing keyword): " + expression
- )
- retlist = sublist[0:i]
- retlist += compressOrDCB(inner + sublist[i+1:], 1)
- return retlist
- elif sublist[i][0] == 'NOT':
- retlist = sublist[0:i]
- retlist += compressOrDCB(
- [('NOT', compressOrDCB([sublist[i][1]])[0])]
- + sublist[i+1:], 1
- )
- return retlist
- elif sublist[i][0] == 'AND':
- retlist = sublist[0:i]
- retlist += compressOrDCB(
- [('AND',
- compressOrDCB([sublist[i][1]])[0],
- compressOrDCB([sublist[i][2]])[0])]
- + sublist[i+1:], 1)
- return retlist
- i += 1
- return sublist[:]
- compressed = compressOrDCB(compressAnd(compressNot(compressBraces(al))))
- if len(compressed) != 1:
- raise ValueError(
- "Expression could not be parsed completely"
- "(probably missing keyword): " + expression
- )
- return compressed[0]
+ """
+ shortname = shortname or self.shortname
+ longname = longname or self.longname
+ mask = self.calcColumn(exprStr, 'm', 'mask')
+ assert isinstance(mask.unit, float)
+ mask = mask.data
+ return self.extractRows(mask, shortname, longname)
- def filter(self, expression):
+ def extractRows(self, mask, shortname, longname):
"""
- Returns a new SampleContainer with filter commands applied to it.
- expression -- can be either a string expression or nested tuples
- of commands. In case expression is a string (or unicode),
- the following syntax holds:
- Let's define
- <atomar> := <value> <CompareOp> <value>
- where <value> is either a SC Column accessed as
- "longname" or "shortname" (including the double quotes)
- or a number or a string representing a Quantity
- (e.g. 300nm). And <CompareOp> can be ==, !=, <, <=, >, >=.
- Then a valid expression <expression> is:
- - <atomar>
- - (<expression>)
- - not <expression>
- - <expression> and <expression>
- - <expression> or <expression>
- - NOT, AND, OR is equivalent to not, and, or
- Precedence is as follows:
- - multiple CompareOps are evaluated:
- e.g. a <= b < c --> (a <= b and b < c)
- - <atomar>
- - braces
- - not
- - and
- - or
- If expression is a nested tuple, syntax is as follows:
- <value> is either ('SCColumn', FieldContainer instance)
- or ('PhysQuant', Quantity instance)
- or ('Number', int float etc.)
- <CompareOp> is in ['==', '!=', ...]
- A valid nested tuple <nt> can be:
- - ('Atomar', <value>, <CompareOp>, <value>)
- - ('NOT', <nt>)
- - ('AND', <nt>, <nt>)
- - ('OR', <nt>, <nt>)
- Precedence is obtained from the way the tuples are nested.
- """
- #determine type of expression:
- from types import StringType, UnicodeType, TupleType
- commands = None
- if isinstance(expression, UnicodeType):
- commands = self._getCommands(expression.encode('utf-8'))
- elif isinstance(expression, StringType):
- commands = self._getCommands(expression)
- elif isinstance(expression, TupleType) or expression == None:
- commands = expression
- else:
- raise TypeError(
- "Expression has to be of StringType, UnicodeType,"
- "TupleType or None. Found " + str(type(expression))
- + " instead!"
- )
- #check for empty commands:
- if commands == None or commands == ():
- return copy.deepcopy(self)
- #generate boolean numpymask from commands using fast numpy methods:
- def evaluateAtomar(atomar):
- left = atomar[1]
- if left[0] == 'SCColumn':
- if left[1].data.ndim != 1:
- raise NotImplementedError(
- 'Comparing columns of dimensions other than one '
- 'is not yet implemented: "' + left[1].longname + '"'
- )
- right = atomar[3]
- if right[0] == 'SCColumn':
- if right[1].data.ndim != 1:
- raise NotImplementedError(
- 'Comparing columns of dimensions other than one '
- 'is not yet implemented: "' + right[1].longname + '"'
- )
- leftvalue = None
- rightvalue = None
- if left[0] == 'SCColumn' and right[0] == 'SCColumn':
- number = right[1].unit/left[1].unit
- if isQuantity(number):
- raise TypeError(
- 'Cannot compare "' + left[1].longname + '" to "'
- + right[1].longname + '".'
- )
- leftvalue = left[1].data
- rightvalue = right[1].data*number
- elif left[0] == 'SCColumn':
- number = right[1]/left[1].unit
- if isQuantity(number):
- raise TypeError(
- 'Cannot compare "' + left[1].longname
- + '" to ' + str(right[1]) + '".'
- )
- leftvalue = left[1].data
- rightvalue = number
- elif right[0] == 'SCColumn':
- number = left[1]/right[1].unit
- if isQuantity(number):
- raise TypeError(
- "Cannot compare " + str(left[1]) + ' to "'
- + right[1].longname + '".'
- )
- leftvalue = number
- rightvalue = right[1].data
- else:
- raise ValueError(
- "At least one argument of '" + atomar[2][1]
- + "' has to be a column."
- )
- if atomar[2] == '==': return leftvalue == rightvalue
- elif atomar[2] == '!=': return leftvalue != rightvalue
- elif atomar[2] == '<=': return leftvalue <= rightvalue
- elif atomar[2] == '<' : return leftvalue < rightvalue
- elif atomar[2] == '>=': return leftvalue >= rightvalue
- elif atomar[2] == '>' : return leftvalue > rightvalue
- raise ValueError, "Invalid atomar expression: " + str(atomar)
+ Return an unsealed SampleContainer that contains only selected rows. The
+ selection is specified via the `mask`.
- def getMaskFromCommands(cmds):
- """
- Returns a boolean numpy mask from given commands.
- cmds -- nested tuples of commands (see SampleContainer.filter())
- """
- if cmds[0] == 'Atomar':
- return evaluateAtomar(cmds)
- elif cmds[0] == 'AND':
- left = getMaskFromCommands(cmds[1])
- right = getMaskFromCommands(cmds[2])
- if left.shape != right.shape:
- raise TypeError(
- "Cannot apply 'and' to columns of different shape: "
- + str(left.shape) + ", " + str(right.shape)
- )
- return numpy.logical_and(left, right)
- elif cmds[0] == 'OR':
- left = getMaskFromCommands(cmds[1])
- right = getMaskFromCommands(cmds[2])
- if left.shape != right.shape:
- raise TypeError(
- "Cannot apply 'or' to columns of different shape: "
- + str(left.shape) + ", " + str(right.shape)
- )
- return numpy.logical_or(left, right)
- elif cmds[0] == 'NOT':
- return numpy.logical_not(getMaskFromCommands(cmds[1]))
- numpymask = getMaskFromCommands(commands)
+ Parameters
+ ----------
+ mask : numpy array of Boolean values
+ The length of the array has to be equal to the length of the columns
+ of the SampleContainer. If the value of mask[n] is
+ True, the nth row is part of the result, else it is discarded.
+
+ shortname, longname : str
+ Specify the short and long name of the resulting FC.
+
+ """
maskedcolumns = []
for col in self.columns:
- maskedcol = None
try:
- maskedcol = col.getMaskedFC(numpymask)
+ maskedcol = col.getMaskedFC(mask)
except ValueError:
raise ValueError(
'Column "' + col.longname + '" has not enough rows!'
@@ -744,11 +449,12 @@
maskedcolumns.append(maskedcol)
#build new SampleContainer from masked columns and return it
result = SampleContainer(maskedcolumns,
- longname=self.longname,
- shortname=self.shortname,
+ longname=longname,
+ shortname=shortname,
attributes=copy.deepcopy(self.attributes))
return result
+
def assertEqual(con1, con2, rtol=1e-5, atol=1e-8):
diagnosis = StringIO.StringIO()
testReport = logging.StreamHandler(diagnosis)
@@ -759,3 +465,179 @@
return True
else:
raise AssertionError, diagnosis.getvalue()
+
+
+class LocationFixingNodeTransformer(NodeTransformer):
+ def visit(self, *args, **kargs):
+ result = NodeTransformer.visit(self, *args, **kargs)
+ from ast import fix_missing_locations
+ fix_missing_locations(result)
+ return result
+
+
+class ReplaceName(LocationFixingNodeTransformer):
+ def __init__(self, sampleContainer):
+ self.localDict = {}
+ self.count = 0
+ self.sc = sampleContainer
+
+ def visit_Call(self, node):
+ from ast import (Name, Load)
+ if isinstance(node.func, Name) and node.func.id.lower() == 'col':
+ newName = self.getName(self.sc[node.args[0].s])
+ return Name(newName, Load())
+
+ def visit_Str(self, node):
+ from ast import (Name, Load)
+ quantity = Quantity(node.s)
+ class QuantityDummy(object):
+ pass
+ dummy = QuantityDummy()
+ dummy.unit = Quantity(1.0, quantity.unit)
+ dummy.data = quantity.value
+ dummy.dimensions = None
+ newName = self.getName(dummy)
+ return Name(newName, Load())
+
+ def getName(self, ref):
+ newName = "N%s" % self.count
+ self.count += 1
+ self.localDict[newName] = ref
+ return newName
+
+
+class ReplaceOperator(LocationFixingNodeTransformer):
+ def __init__(self, localDict):
+ self.localDict = localDict
+
+ def visit_BinOp(self, node):
+ from ast import (Add, Sub, BinOp)
+ self.generic_visit(node)
+ unitcalc = UnitCalculator(self.localDict)
+ leftUD = unitcalc.getUnitAndDim(node.left)
+ rightUD = unitcalc.getUnitAndDim(node.right)
+ checkDimensions(leftUD[1], rightUD[1])
+ if isinstance(node.op,(Add, Sub)):
+ factor = rightUD[0] / leftUD[0]
+ right = self.withFactor(factor, node.right)
+ binOp = BinOp(node.left, node.op, right)
+ return binOp
+ else:
+ return node
+
+ def visit_Compare(self, node):
+ from ast import Compare
+ self.generic_visit(node)
+ unitcalc = UnitCalculator(self.localDict)
+ leftUD = unitcalc.getUnitAndDim(node.left)
+ listUD = [unitcalc.getUnitAndDim(comp) for comp in node.comparators]
+ nonNoneDims = [ud[1] for ud in listUD + [leftUD] if ud[1] is not None]
+ for dims in nonNoneDims:
+ checkDimensions(nonNoneDims[0], dims)
+ factorlist = [ud[0] / leftUD[0] for ud in listUD]
+ newComplist = [self.withFactor(*t) \
+ for t in zip(factorlist, node.comparators)]
+ compOp = Compare(node.left, node.ops, newComplist)
+ compOpTrans = self.compBreaker(compOp)
+ return compOpTrans
+
+ def withFactor(self, factor, node):
+ from ast import (BinOp, Num, Mult)
+ if not isinstance(factor, float):
+ raise ValueError('Incompatible units!')
+ if factor == 1.0:
+ return node
+ return BinOp(Num(factor), Mult(), node)
+
+ def compBreaker(self, node):
+ from ast import (Compare, BinOp, BitAnd)
+ assert isinstance(node, Compare)
+ if len(node.comparators) == 1:
+ return node
+ else:
+ comp1 = Compare(node.left, node.ops[0:1],
+ node.comparators[0:1])
+ comp2 = Compare(node.comparators[0],
+ node.ops[1:], node.comparators[1:])
+ newNode = BinOp(comp1, BitAnd(), self.compBreaker(comp2))
+ return newNode
+
+
+class UnitCalculator(object):
+ def __init__(self, localDict):
+ self.localDict = localDict
+
+ def getUnitAndDim(self, node):
+ from ast import (Expression, Name, Num,
+ BinOp, Add, Mult, Div, Sub,
+ Compare, BoolOp, UnaryOp,
+ BitOr, BitXor, BitAnd)
+ if isinstance(node, Expression):
+ return self.getUnitAndDim(node.body)
+ elif isinstance(node, Name):
+ if node.id in ['True', 'False']:
+ return (1.0, None)
+ else:
+ column = self.localDict[node.id]
+ return (column.unit, column.dimensions)
+ elif isinstance(node, Num):
+ return (1.0, None)
+ elif isinstance(node, BinOp):
+ left = self.getUnitAndDim(node.left)
+ right = self.getUnitAndDim(node.right)
+ dimensions = checkDimensions(left[1], right[1])
+ if isinstance(node.op, (Add, Sub)):
+ if not isinstance(left[0] / right[0], float):
+ raise ValueError("units %s, %s not compatible" \
+ % (left, right))
+ unit = left[0]
+ elif isinstance(node.op, Mult):
+ unit = left[0] * right[0]
+ elif isinstance(node.op, Div):
+ unit = left[0] / right[0]
+ elif isinstance(node.op, (BitOr, BitXor, BitAnd)):
+ if not isinstance(left[0], float):
+ raise ValueError(
+ "Type %s cannot be interpreted as a Boolean" % left)
+ if not isinstance(right[0], float):
+ raise ValueError(
+ "Type %s cannot be interpreted as a Boolean" % right)
+ unit = 1.0
+ else:
+ raise NotImplementedError()
+ return (unit, dimensions)
+ elif isinstance(node, Compare):
+ left = self.getUnitAndDim(node.left)
+ nonNoneDims = []
+ if left[1] is not None:
+ nonNoneDims.append(left[1])
+ for comparator in node.comparators:
+ right = self.getUnitAndDim(comparator)
+ if right[1] is not None:
+ nonNoneDims.append(right[1])
+ if not isinstance(left[0] / right[0], float):
+ raise ValueError("units %s, %s not compatible" \
+ % (left[0], right[0]))
+ if len(nonNoneDims) >= 1:
+ for dims in nonNoneDims:
+ checkDimensions(nonNoneDims[0], dims)
+ dimensions = nonNoneDims[0]
+ else:
+ dimensions = None
+ return (1.0, dimensions)
+ elif isinstance(node, BoolOp):
+ raise NotImplementedError(
+ 'BoolOps not supported. Use bitwise ops instead (&, |)!')
+ elif isinstance(node, UnaryOp):
+ return self.getUnitAndDim(node.operand)
+ else:
+ raise NotImplementedError()
+
+
+def checkDimensions(dimensions1, dimensions2):
+ if dimensions1 is not None and dimensions2 is not None and \
+ dimensions1 != dimensions2:
+ msg = 'Dimensions "%s" and "%s" do not match!' \
+ % (dimensions1, dimensions2)
+ raise ValueError(msg)
+ return dimensions1 or dimensions2
Modified: trunk/src/pyphant/pyphant/core/FieldContainer.py
===================================================================
--- trunk/src/pyphant/pyphant/core/FieldContainer.py 2010-09-13 08:56:34 UTC (rev 699)
+++ trunk/src/pyphant/pyphant/core/FieldContainer.py 2011-05-23 12:48:36 UTC (rev 700)
@@ -288,12 +288,15 @@
if m == None:
m = hashlib.md5()
super(FieldContainer, self).generateHash(m)
- m.update(str(self.data.tolist()))
+ #m.update(str(self.data.tolist()))
+ m.update(self.data.dumps())
m.update(str(self.unit))
if self.error!=None:
- m.update(str(self.error.tolist()))
+ #m.update(str(self.error.tolist()))
+ m.update(self.error.dumps())
if self.mask!=None:
- m.update(str(self.mask.tolist()))
+ #m.update(str(self.mask.tolist()))
+ m.update(self.mask.dumps())
[m.update(dim.hash) for dim in self._dimensions]
return enc(m.hexdigest())
@@ -648,8 +651,8 @@
def getMaskedFC(self, numpymask):
"""
- Returns a new FieldContainer instance that emerges from this instance
- by clipping along the primary axis according to the
+ Return an unsealed FieldContainer instance that emerges from
+ this instance by clipping along the primary axis according to the
entries in the parameter numpymask, i.e. all entries where numpymask
is set to False are discarded.
numpymask -- Numpy array with Boolean values
Modified: trunk/src/pyphant/pyphant/core/H5FileHandler.py
===================================================================
--- trunk/src/pyphant/pyphant/core/H5FileHandler.py 2010-09-13 08:56:34 UTC (rev 699)
+++ trunk/src/pyphant/pyphant/core/H5FileHandler.py 2011-05-23 12:48:36 UTC (rev 700)
@@ -121,7 +121,7 @@
try:
resNode._g_checkHasChild('dimensions')
except tables.NoSuchNodeError:
- return True
+ return True
return False
def loadDataContainer(self, dcId):
@@ -220,6 +220,9 @@
summary['attributes'] = attributes
return summary
+ def loadRecipe(self):
+ return PyTablesPersister.loadRecipe(self.handle)
+
def saveDataContainer(self, result):
"""
Saves a given DataContainer instance to the HDF5 file.
Modified: trunk/src/pyphant/pyphant/core/Helpers.py
===================================================================
--- trunk/src/pyphant/pyphant/core/Helpers.py 2010-09-13 08:56:34 UTC (rev 699)
+++ trunk/src/pyphant/pyphant/core/Helpers.py 2011-05-23 12:48:36 UTC (rev 700)
@@ -40,8 +40,12 @@
if homedir == '~':
homedir = os.getcwdu()
path = os.path.join(homedir, '.pyphant', subdir)
- if not os.path.isdir(path):
- os.makedirs(path)
+ # Create the dir in a multi process save way:
+ try:
+ os.makedirs(path) #<-- ignores EEXIST in all but top recursion levels
+ except OSError, ose:
+ if ose.errno != os.errno.EEXIST:
+ raise
return path
def getUsername():
@@ -154,3 +158,28 @@
output = plug.getResult()
socket.pullPlug()
return output
+
+def makeSC(column_data, longnames, shortnames, longname, shortname,
+ attributes={}):
+ unzipped = zip(*column_data)
+ assert len(unzipped) == len(longnames) == len(shortnames)
+ def get_column_fc(col, ln, sn):
+ try:
+ from pyphant.quantities import Quantity
+ unit = Quantity(1.0, col[0].unit)
+ data = [quant.value for quant in col]
+ except (KeyError, AttributeError):
+ unit = 1
+ data = col
+ from numpy import array
+ from pyphant.core.DataContainer import FieldContainer
+ fc = FieldContainer(data=array(data), unit=unit,
+ longname=ln, shortname=sn)
+ return fc
+ columns = [get_column_fc(col, ln, sn) for col, ln, sn \
+ in zip(unzipped, longnames, shortnames)]
+ from pyphant.core.DataContainer import SampleContainer
+ sc = SampleContainer(longname=longname, shortname=shortname,
+ attributes=attributes, columns=columns)
+ sc.seal()
+ return sc
Modified: trunk/src/pyphant/pyphant/core/KnowledgeManager.py
===================================================================
--- trunk/src/pyphant/pyphant/core/KnowledgeManager.py 2010-09-13 08:56:34 UTC (rev 699)
+++ trunk/src/pyphant/pyphant/core/KnowledgeManager.py 2011-05-23 12:48:36 UTC (rev 700)
@@ -198,11 +198,14 @@
for fname in [afname for afname in files if afname.endswith('.h5')]:
flist.append(os.path.realpath(os.path.join(directory, fname)))
os.path.walk(getPyphantPath(KM_PATH), accumulate_files, file_list)
- from wx import (ProgressDialog, PyNoAppError)
try:
- pdial = ProgressDialog('Rebuilding index...', ' ' * 100,
- maximum=len(file_list))
- except PyNoAppError:
+ from wx import (ProgressDialog, PyNoAppError)
+ try:
+ pdial = ProgressDialog('Rebuilding index...', ' ' * 100,
+ maximum=len(file_list))
+ except PyNoAppError:
+ pdial = None
+ except ImportError:
pdial = None
count = 1
for realname in file_list:
Modified: trunk/src/pyphant/pyphant/core/Worker.py
===================================================================
--- trunk/src/pyphant/pyphant/core/Worker.py 2010-09-13 08:56:34 UTC (rev 699)
+++ trunk/src/pyphant/pyphant/core/Worker.py 2011-05-23 12:48:36 UTC (rev 700)
@@ -81,9 +81,12 @@
_plugs=[]
_params=[]
DEFAULT_ANNOTATIONS={"pos":(0,0)}
- def __init__(self, parent=None, annotations={}):
- self._annotations=annotations
- map(lambda k: self._annotations.setdefault(k, Worker.DEFAULT_ANNOTATIONS[k]),
+ def __init__(self, parent=None, annotations=None):
+ if annotations is None:
+ annotations = {}
+ self._annotations = annotations
+ map(lambda k: self._annotations.setdefault(
+ k, Worker.DEFAULT_ANNOTATIONS[k]),
Worker.DEFAULT_ANNOTATIONS.keys())
self.parent=parent
self.initSockets(self._sockets)
@@ -144,7 +147,7 @@
self._params={}
self._order=[]
self.addParam('name',Param.createParam(self,'name','Name',
- self.__class__.__name__))
+ self.name))
for (name, displayName, value, subtype) in params:
p=Param.createParam(self, name, displayName, value, subtype)
setattr(self, 'param'+self.upperFirstLetter(name), p)
Deleted: trunk/src/pyphant/pyphant/core/XMLHandler.py
===================================================================
--- trunk/src/pyphant/pyphant/core/XMLHandler.py 2010-09-13 08:56:34 UTC (rev 699)
+++ trunk/src/pyphant/pyphant/core/XMLHandler.py 2011-05-23 12:48:36 UTC (rev 700)
@@ -1,88 +0,0 @@
-# -*- coding: utf-8 -*-
-
-# Copyright (c) 2006-2009, Rectorate of the University of Freiburg
-# All rights reserved.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-#
-# * Redistributions of source code must retain the above copyright
-# notice, this list of conditions and the following disclaimer.
-# * Redistributions in binary form must reproduce the above copyright
-# notice, this list of conditions and the following disclaimer in the
-# documentation and/or other materials provided with the distribution.
-# * Neither the name of the Freiburg Materials Research Center,
-# University of Freiburg nor the names of its contributors may be used to
-# endorse or promote products derived from this software without specific
-# prior written permission.
-#
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
-# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
-# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
-# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-"""
-TODO
-"""
-__id__ = "$Id$"
-__author__ = "$Author$"
-__version__ = "$Revision$"
-# $Source$:
-
-import xml.sax
-
-
-class XMLElement(object):
-
- def __init__(self, name, attrs, parent, content=''):
- self.name = name
- self.attributes = attrs
- self.parent = parent
- self.children = {}
- self.content = content
- if parent != None:
- parent[name] = self
-
- def __getitem__(self, key):
- return self.children[key]
-
- def __setitem__(self, key, item):
- self.children[key] = item
-
-
-class XMLHandler(xml.sax.handler.ContentHandler):
-
- def __init__(self):
- self.current_element = None
- self.root_element = None
-
- def startElement(self, name, attrs):
- if self.root_element == None:
- element = XMLElement(name, attrs, None)
- self.root_element = element
- self.current_element = element
- else:
- element = XMLElement(name, attrs, self.current_element)
- self.current_element = element
-
- def endElement(self, name):
- assert name == self.current_element.name
- self.current_element = self.current_element.parent
-
- def characters(self, content):
- if self.current_element != None:
- self.current_element.content += content
-
-
-def getXMLRoot(filename_or_stream):
- handler = XMLHandler()
- xml.sax.parse(filename_or_stream, handler)
- return handler.root_element
Deleted: trunk/src/pyphant/pyphant/core/ZStackManager.py
===================================================================
--- trunk/src/pyphant/pyphant/core/ZStackManager.py 2010-09-13 08:56:34 UTC (rev 699)
+++ trunk/src/pyphant/pyphant/core/ZStackManager.py 2011-05-23 12:48:36 UTC (rev 700)
@@ -1,300 +0,0 @@
-#!/usr/bin/env python2.5
-# -*- coding: utf-8 -*-
-
-# Copyright (c) 2006-2009, Rectorate of the University of Freiburg
-# All rights reserved.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-#
-# * Redistributions of source code must retain the above copyright
-# notice, this list of conditions and the following disclaimer.
-# * Redistributions in binary form must reproduce the above copyright
-# notice, this list of conditions and the following disclaimer in the
-# documentation and/or other materials provided with the distribution.
-# * Neither the name of the Freiburg Materials Research Center,
-# University of Freiburg nor the names of its contributors may be used to
-# endorse or promote products derived from this software without specific
-# prior written permission.
-#
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
-# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
-# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
-# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-u"""Provides ZStackManager
-"""
-
-__id__ = "$Id$".replace('$','')
-__author__ = "$Author$".replace('$','')
-__version__ = "$Revision$".replace('$','')
-# $Source$
-
-
-from pyphant.quantities import Quantity
-from pyphant.core.DataContainer import (FieldContainer, SampleContainer)
-import scipy
-import Image
-from pyphant.core.KnowledgeManager import KnowledgeManager
-import os
-import re
-kmanager = KnowledgeManager.getInstance()
-
-
-class ZStack(object):
- def __init__(self, sc_id=None, meta=None, temporary=False):
- """Initializes a ZStack from an existing id or metadata"""
- assert (sc_id is None) is not (meta is None)
- self.temporary = temporary
- if sc_id is not None:
- self.repr_sc = kmanager.getDataContainer(sc_id)
- else:
- self.repr_sc = self._import_zstack(meta)
-
- @staticmethod
- def _get_image_fcs(images_meta, temporary=False):
- zvalues = []
- emd5s = []
- files = []
- from wx import (ProgressDialog, PyNoAppError)
- try:
- pdial = ProgressDialog('Importing ZStack...', ' ' * 50,
- maximum=len(images_meta))
- except PyNoAppError:
- pdial = None
- count = 1
- for img_meta in images_meta:
- if pdial is not None:
- pdial.Update(count, os.path.basename(img_meta['imgFilename']))
- count += 1
- files.append(img_meta['xmlFilename'])
- img = Image.open(img_meta['imgFilename'])
- data = scipy.misc.fromimage(img, flatten=True)
- zvalue = img_meta['z-pos']
- yunit = Quantity(1.0, img_meta['height'].unit)
- xunit = Quantity(1.0, img_meta['width'].unit)
- ydata = scipy.arange(img_meta['height[pixel]']) \
- * img_meta['y-factor'].inUnitsOf(yunit.unit).value \
- + img_meta['y-pos'].inUnitsOf(yunit.unit).value
- xdata = scipy.arange(img_meta['width[pixel]']) \
- * img_meta['x-factor'].inUnitsOf(xunit.unit).value \
- + img_meta['x-pos'].inUnitsOf(xunit.unit).value
- dimensions = [FieldContainer(ydata,
- unit=yunit,
- longname=u'y-axis',
- shortname=u'y'),
- FieldContainer(xdata,
- unit=xunit,
- longname=u'x-axis',
- shortname=u'x')]
- fcattr = {'vmin':0, 'vmax':255}
- fcattr.update(img_meta)
- img_fc = FieldContainer(data=data,
- longname=os.path.basename(
- img_meta['imgFilename']),
- shortname="i",
- dimensions=dimensions, attributes=fcattr)
- img_fc.seal()
- kmanager.registerDataContainer(img_fc, temporary=temporary)
- emd5s.append(img_fc.id)
- zvalues.append(zvalue.value)
- if len(zvalues) == 0:
- return None, None, None
- zfc = FieldContainer(scipy.array(zvalues), longname='z-value',
- shortname='z', unit=Quantity(1.0, zvalue.unit))
- filefc = FieldContainer(scipy.array(files), longname='filename',
- shortname='f')
- emd5fc = FieldContainer(scipy.array(emd5s), longname='emd5',
- shortname='i')
- if pdial is not None:
- pdial.Destroy()
- return zfc, filefc, emd5fc
-
- def _import_zstack(self, meta):
- zfc, filefc, emd5fc = ZStack._get_image_fcs(meta, self.temporary)
- if zfc == None:
- return None
- attributes = {}
- attributes['ZStackType'] = 'RawSC'
- attributes['xmlFilename'] = meta[0]['xmlFilename']
- attributes['crystal'] = meta[0]['crystal']
- ssc = SampleContainer([zfc, filefc, emd5fc],
- meta[0]['ZStackName'],
- "z",
- attributes)
- ssc.seal()
- kmanager.registerDataContainer(ssc, temporary=self.temporary)
- return ssc
-
-
-class ZStackManager(object):
- def importZStack(self, xmlFName, name, crystal, temporary=False):
- metaReader = getMetaReader(xmlFName, name, crystal)
- meta = metaReader.getMeta()
- return ZStack(meta=meta, temporary=temporary)
-
- def getZStacks(self):
- """Returns a list of all ZStacks in the pool"""
- search_dict = {'type':'sample', 'attributes':{'ZStackType':'RawSC'}}
- search_result = kmanager.search(['id'], search_dict)
- if len(search_result) == 0:
- return []
- return [ZStack(zs_id[0]) for zs_id in search_result]
-
- def getZStackByName(self, name):
- search_dict = {'type':'sample', 'attributes':{'ZStackType':'RawSC'},
- 'longname':name}
- sresult = kmanager.search(['id'], search_dict)
- if sresult == []:
- raise ValueError("There is no ZStack called %s!" \
- % name)
- return ZStack(sc_id=sresult[0][0])
-
-
-class MetaReader(object):
- def __init__(self, xmlFName, name, crystal):
- self.xmlFN...
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