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bugfixes

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MetaArray update - no longer subclass of ndarray
This commit is contained in:
Luke Campagnola 2012-05-23 20:20:54 -04:00
parent 194f90aa4d
commit 4d1a5ded1b
5 changed files with 256 additions and 184 deletions
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11
graphicsItems/GraphicsWidget.py
View File

@ -16,11 +16,12 @@ class GraphicsWidget(GraphicsItem, QtGui.QGraphicsWidget):
GraphicsItem.__init__(self) GraphicsItem.__init__(self)
GraphicsScene.registerObject(self) ## workaround for pyqt bug in graphicsscene.items() GraphicsScene.registerObject(self) ## workaround for pyqt bug in graphicsscene.items()
def itemChange(self, change, value): ## Removed because this causes segmentation faults. Don't know why.
ret = QtGui.QGraphicsWidget.itemChange(self, change, value) # def itemChange(self, change, value):
if change in [self.ItemParentHasChanged, self.ItemSceneHasChanged]: # ret = QtGui.QGraphicsWidget.itemChange(self, change, value) ## segv occurs here
self._updateView() # if change in [self.ItemParentHasChanged, self.ItemSceneHasChanged]:
return ret # self._updateView()
# return ret
#def getMenu(self): #def getMenu(self):
#pass #pass

2
graphicsItems/GridItem.py
View File

@ -22,7 +22,7 @@ class GridItem(UIGraphicsItem):
def viewRangeChanged(self): def viewRangeChanged(self):
GraphicsObject.viewRangeChanged(self) UIGraphicsItem.viewRangeChanged(self)
self.picture = None self.picture = None
#UIGraphicsItem.viewRangeChanged(self) #UIGraphicsItem.viewRangeChanged(self)
#self.update() #self.update()

17
graphicsItems/PlotDataItem.py
View File

@ -1,9 +1,4 @@
try: import pyqtgraph.metaarray as metaarray
import metaarray
HAVE_METAARRAY = True
except:
HAVE_METAARRAY = False
from pyqtgraph.Qt import QtCore from pyqtgraph.Qt import QtCore
from .GraphicsObject import GraphicsObject from .GraphicsObject import GraphicsObject
from .PlotCurveItem import PlotCurveItem from .PlotCurveItem import PlotCurveItem
@ -252,6 +247,7 @@ class PlotDataItem(GraphicsObject):
if len(args) == 1: if len(args) == 1:
data = args[0] data = args[0]
dt = dataType(data) dt = dataType(data)
print "plot:", dt, type(data)
if dt == 'empty': if dt == 'empty':
pass pass
elif dt == 'listOfValues': elif dt == 'listOfValues':
@ -493,9 +489,10 @@ def dataType(obj):
return 'empty' return 'empty'
if isSequence(obj): if isSequence(obj):
first = obj[0] first = obj[0]
if isinstance(obj, np.ndarray):
if HAVE_METAARRAY and isinstance(obj, metaarray.MetaArray): if isinstance(obj, metaarray.MetaArray):
return 'MetaArray' return 'MetaArray'
elif isinstance(obj, np.ndarray):
if obj.ndim == 1: if obj.ndim == 1:
if obj.dtype.names is None: if obj.dtype.names is None:
return 'listOfValues' return 'listOfValues'
@ -514,7 +511,7 @@ def dataType(obj):
def isSequence(obj): def isSequence(obj):
return isinstance(obj, list) or isinstance(obj, np.ndarray) return isinstance(obj, list) or isinstance(obj, np.ndarray) or isinstance(obj, metaarray.MetaArray)

10
imageview/ImageView.py
View File

@ -29,6 +29,13 @@ import pyqtgraph.debug as debug
from pyqtgraph.SignalProxy import SignalProxy from pyqtgraph.SignalProxy import SignalProxy
try:
import pyqtgraph.metaarray as metaarray
HAVE_METAARRAY = True
except:
HAVE_METAARRAY = False
class PlotROI(ROI): class PlotROI(ROI):
def __init__(self, size): def __init__(self, size):
ROI.__init__(self, pos=[0,0], size=size, scaleSnap=True, translateSnap=True) ROI.__init__(self, pos=[0,0], size=size, scaleSnap=True, translateSnap=True)
@ -188,6 +195,9 @@ class ImageView(QtGui.QWidget):
""" """
prof = debug.Profiler('ImageView.setImage', disabled=True) prof = debug.Profiler('ImageView.setImage', disabled=True)
if HAVE_METAARRAY and isinstance(img, metaarray.MetaArray):
img = img.asarray()
if not isinstance(img, np.ndarray): if not isinstance(img, np.ndarray):
raise Exception("Image must be specified as ndarray.") raise Exception("Image must be specified as ndarray.")
self.image = img self.image = img

400
metaarray/MetaArray.py
View File

@ -57,7 +57,7 @@ class sliceGenerator:
SLICER = sliceGenerator() SLICER = sliceGenerator()
class MetaArray(np.ndarray): class MetaArray(object):
"""N-dimensional array with meta data such as axis titles, units, and column names. """N-dimensional array with meta data such as axis titles, units, and column names.
May be initialized with a file name, a tuple representing the dimensions of the array, May be initialized with a file name, a tuple representing the dimensions of the array,
@ -109,94 +109,91 @@ class MetaArray(np.ndarray):
@staticmethod @staticmethod
def isNameType(var): def isNameType(var):
return any([isinstance(var, t) for t in MetaArray.nameTypes]) return any([isinstance(var, t) for t in MetaArray.nameTypes])
## methods to wrap from embedded ndarray / HDF5
wrapMethods = set(['__eq__', '__ne__', '__le__', '__lt__', '__ge__', '__gt__'])
def __new__(subtype, data=None, file=None, info=None, dtype=None, copy=False, **kwargs): def __init__(self, data=None, info=None, dtype=None, file=None, copy=False, **kwargs):
if data is not None: object.__init__(self)
if type(data) is tuple: #self._infoOwned = False
subarr = np.empty(data, dtype=dtype) self._isHDF = False
else:
subarr = np.array(data, dtype=dtype, copy=copy)
subarr = subarr.view(subtype)
#### Sanity checks on info
if info is not None:
try:
info = list(info)
except:
raise Exception("Info must be a list of axis specifications")
if len(info) < subarr.ndim+1:
info.extend([{}]*(subarr.ndim+1-len(info)))
elif len(info) > subarr.ndim+1:
raise Exception("Info parameter must be list of length ndim+1 or less.")
for i in range(len(info)):
if not isinstance(info[i], dict):
if info[i] is None:
info[i] = {}
else:
raise Exception("Axis specification must be Dict or None")
if i < subarr.ndim and 'values' in info[i]:
if type(info[i]['values']) is list:
info[i]['values'] = np.array(info[i]['values'])
elif type(info[i]['values']) is not np.ndarray:
raise Exception("Axis values must be specified as list or ndarray")
if info[i]['values'].ndim != 1 or info[i]['values'].shape[0] != subarr.shape[i]:
raise Exception("Values array for axis %d has incorrect shape. (given %s, but should be %s)" % (i, str(info[i]['values'].shape), str((subarr.shape[i],))))
if i < subarr.ndim and 'cols' in info[i]:
if not isinstance(info[i]['cols'], list):
info[i]['cols'] = list(info[i]['cols'])
if len(info[i]['cols']) != subarr.shape[i]:
raise Exception('Length of column list for axis %d does not match data. (given %d, but should be %d)' % (i, len(info[i]['cols']), subarr.shape[i]))
subarr._info = info
elif hasattr(data, '_info'):
subarr._info = data._info
elif file is not None:
## decide which read function to use
fd = open(file, 'rb')
magic = fd.read(8)
if magic == '\x89HDF\r\n\x1a\n':
fd.close()
return MetaArray._readHDF5(file, subtype, **kwargs)
else:
fd.seek(0)
meta = MetaArray._readMeta(fd)
if 'version' in meta:
ver = meta['version']
else:
ver = 1
rFuncName = '_readData%s' % str(ver)
if not hasattr(MetaArray, rFuncName):
raise Exception("This MetaArray library does not support array version '%s'" % ver)
rFunc = getattr(MetaArray, rFuncName)
subarr = rFunc(fd, meta, subtype, **kwargs)
return subarr
def __array_finalize__(self,obj):
## array_finalize is called every time a MetaArray is created
## (whereas __new__ is not necessarily called every time)
## obj is the object from which this array was generated (for example, when slicing or view()ing) if file is not None:
self._data = None
self.readFile(file, **kwargs)
if self._data is None:
raise Exception("File read failed: %s" % file)
else:
self._info = info
if isinstance(data, MetaArray):
self._info = data._info
self._data = data.asarray()
elif isinstance(data, tuple): ## create empty array with specified shape
self._data = np.empty(data, dtype=dtype)
else:
self._data = np.array(data, dtype=dtype, copy=copy)
## run sanity checks on info structure
self.checkInfo()
def checkInfo(self):
info = self._info
if info is None:
if self._data is None:
return
else:
self._info = [{} for i in range(self.ndim)]
return
else:
try:
info = list(info)
except:
raise Exception("Info must be a list of axis specifications")
if len(info) < self.ndim+1:
info.extend([{}]*(self.ndim+1-len(info)))
elif len(info) > self.ndim+1:
raise Exception("Info parameter must be list of length ndim+1 or less.")
for i in range(len(info)):
if not isinstance(info[i], dict):
if info[i] is None:
info[i] = {}
else:
raise Exception("Axis specification must be Dict or None")
if i < self.ndim and 'values' in info[i]:
if type(info[i]['values']) is list:
info[i]['values'] = np.array(info[i]['values'])
elif type(info[i]['values']) is not np.ndarray:
raise Exception("Axis values must be specified as list or ndarray")
if info[i]['values'].ndim != 1 or info[i]['values'].shape[0] != self.shape[i]:
raise Exception("Values array for axis %d has incorrect shape. (given %s, but should be %s)" % (i, str(info[i]['values'].shape), str((self.shape[i],))))
if i < self.ndim and 'cols' in info[i]:
if not isinstance(info[i]['cols'], list):
info[i]['cols'] = list(info[i]['cols'])
if len(info[i]['cols']) != self.shape[i]:
raise Exception('Length of column list for axis %d does not match data. (given %d, but should be %d)' % (i, len(info[i]['cols']), self.shape[i]))
#def __array_finalize__(self,obj):
### array_finalize is called every time a MetaArray is created
### (whereas __new__ is not necessarily called every time)
# We use the getattr method to set a default if 'obj' doesn't have the 'info' attribute ### obj is the object from which this array was generated (for example, when slicing or view()ing)
#print "Create new MA from object", str(type(obj))
#import traceback ## We use the getattr method to set a default if 'obj' doesn't have the 'info' attribute
#traceback.print_stack() ##print "Create new MA from object", str(type(obj))
#print "finalize", type(self), type(obj) ##import traceback
if not hasattr(self, '_info'): ##traceback.print_stack()
#if isinstance(obj, MetaArray): ##print "finalize", type(self), type(obj)
#print " copy info:", obj._info #if not hasattr(self, '_info'):
self._info = getattr(obj, '_info', [{}]*(obj.ndim+1)) ##if isinstance(obj, MetaArray):
self._infoOwned = False ## Do not make changes to _info until it is copied at least once ##print " copy info:", obj._info
#print " self info:", self._info #self._info = getattr(obj, '_info', [{}]*(obj.ndim+1))
#self._infoOwned = False ## Do not make changes to _info until it is copied at least once
##print " self info:", self._info
# We could have checked first whether self._info was already defined: ## We could have checked first whether self._info was already defined:
#if not hasattr(self, 'info'): ##if not hasattr(self, 'info'):
# self._info = getattr(obj, 'info', {}) ## self._info = getattr(obj, 'info', {})
def __getitem__(self, ind): def __getitem__(self, ind):
@ -206,80 +203,122 @@ class MetaArray(np.ndarray):
nInd = self._interpretIndexes(ind) nInd = self._interpretIndexes(ind)
#print "Indexes:", nInd #a = np.ndarray.__getitem__(self, nInd)
try: a = self._data[nInd]
a = np.ndarray.__getitem__(self, nInd) if len(nInd) == self.ndim:
except: if np.all([not isinstance(ind, slice) for ind in nInd]): ## no slices; we have requested a single value from the array
#print nInd, self.shape return a
raise #if type(a) != type(self._data) and not isinstance(a, np.ndarray): ## indexing returned single value
if type(a) == type(self): ## generate new info array #return a
#print " new MA:", type(a), a.shape
a._info = [] ## indexing returned a sub-array; generate new info array to go with it
extraInfo = self._info[-1].copy() #print " new MA:", type(a), a.shape
for i in range(0, len(nInd)): ## iterate over all axes info = []
#print " axis", i extraInfo = self._info[-1].copy()
if type(nInd[i]) in [slice, list] or isinstance(nInd[i], np.ndarray): ## If the axis is sliced, keep the info but chop if necessary for i in range(0, len(nInd)): ## iterate over all axes
#print " slice axis", i, nInd[i] #print " axis", i
#a._info[i] = self._axisSlice(i, nInd[i]) if type(nInd[i]) in [slice, list] or isinstance(nInd[i], np.ndarray): ## If the axis is sliced, keep the info but chop if necessary
#print " info:", a._info[i] #print " slice axis", i, nInd[i]
a._info.append(self._axisSlice(i, nInd[i])) #a._info[i] = self._axisSlice(i, nInd[i])
else: ## If the axis is indexed, then move the information from that single index to the last info dictionary #print " info:", a._info[i]
#print "indexed:", i, nInd[i], type(nInd[i]) info.append(self._axisSlice(i, nInd[i]))
newInfo = self._axisSlice(i, nInd[i]) else: ## If the axis is indexed, then move the information from that single index to the last info dictionary
name = None #print "indexed:", i, nInd[i], type(nInd[i])
colName = None newInfo = self._axisSlice(i, nInd[i])
for k in newInfo: name = None
if k == 'cols': colName = None
if 'cols' not in extraInfo: for k in newInfo:
extraInfo['cols'] = [] if k == 'cols':
extraInfo['cols'].append(newInfo[k]) if 'cols' not in extraInfo:
if 'units' in newInfo[k]: extraInfo['cols'] = []
extraInfo['units'] = newInfo[k]['units'] extraInfo['cols'].append(newInfo[k])
if 'name' in newInfo[k]: if 'units' in newInfo[k]:
colName = newInfo[k]['name'] extraInfo['units'] = newInfo[k]['units']
elif k == 'name': if 'name' in newInfo[k]:
name = newInfo[k] colName = newInfo[k]['name']
else: elif k == 'name':
if k not in extraInfo: name = newInfo[k]
extraInfo[k] = newInfo[k] else:
if k not in extraInfo:
extraInfo[k] = newInfo[k] extraInfo[k] = newInfo[k]
if 'name' not in extraInfo: extraInfo[k] = newInfo[k]
if name is None: if 'name' not in extraInfo:
if colName is not None: if name is None:
extraInfo['name'] = colName if colName is not None:
extraInfo['name'] = colName
else:
if colName is not None:
extraInfo['name'] = str(name) + ': ' + str(colName)
else: else:
if colName is not None: extraInfo['name'] = name
extraInfo['name'] = str(name) + ': ' + str(colName)
else:
extraInfo['name'] = name #print "Lost info:", newInfo
#a._info[i] = None
#if 'name' in newInfo:
#print "Lost info:", newInfo #a._info[-1][newInfo['name']] = newInfo
#a._info[i] = None info.append(extraInfo)
#if 'name' in newInfo:
#a._info[-1][newInfo['name']] = newInfo #self._infoOwned = False
a._info.append(extraInfo) #while None in a._info:
#a._info.remove(None)
self._infoOwned = False return MetaArray(a, info=info)
#while None in a._info:
#a._info.remove(None)
return a
@property
def ndim(self):
return len(self.shape) ## hdf5 objects do not have ndim property.
@property
def shape(self):
return self._data.shape
@property
def dtype(self):
return self._data.dtype
def __len__(self):
return len(self._data)
def __getslice__(self, *args): def __getslice__(self, *args):
return self.__getitem__(slice(*args)) return self.__getitem__(slice(*args))
def __setitem__(self, ind, val): def __setitem__(self, ind, val):
nInd = self._interpretIndexes(ind) nInd = self._interpretIndexes(ind)
try: try:
return np.ndarray.__setitem__(self.view(np.ndarray), nInd, val) self._data[nInd] = val
except: except:
print(self, nInd, val) print(self, nInd, val)
raise raise
#def __getattr__(self, attr): def __getattr__(self, attr):
#if attr in ['round']: if attr in self.wrapMethods:
return getattr(self._data, attr)
else:
raise AttributeError(attr)
#return lambda *args, **kwargs: MetaArray(getattr(a.view(ndarray), attr)(*args, **kwargs) #return lambda *args, **kwargs: MetaArray(getattr(a.view(ndarray), attr)(*args, **kwargs)
def __eq__(self, b):
if isinstance(b, MetaArray):
b = b.asarray()
return self._data == b
def __ne__(self, b):
if isinstance(b, MetaArray):
b = b.asarray()
return self._data != b
def asarray(self):
if isinstance(self._data, np.ndarray):
return self._data
else:
return np.array(self._data)
def view(self, typ):
## deprecated; kept for backward compatibility
if typ is np.ndarray:
return self.asarray()
else:
raise Exception('invalid view type: %s' % str(typ))
def axisValues(self, axis): def axisValues(self, axis):
"""Return the list of values for an axis""" """Return the list of values for an axis"""
@ -591,8 +630,8 @@ class MetaArray(np.ndarray):
def axisCollapsingFn(self, fn, axis=None, *args, **kargs): def axisCollapsingFn(self, fn, axis=None, *args, **kargs):
arr = self.view(np.ndarray) #arr = self.view(np.ndarray)
fn = getattr(arr, fn) fn = getattr(self._data, fn)
if axis is None: if axis is None:
return fn(axis, *args, **kargs) return fn(axis, *args, **kargs)
else: else:
@ -623,12 +662,37 @@ class MetaArray(np.ndarray):
order = order + list(range(len(order), self.ndim)) order = order + list(range(len(order), self.ndim))
try: try:
return MetaArray(self.view(np.ndarray).transpose(order), info=info) if self._isHDF:
return MetaArray(np.array(self._data).transpose(order), info=info)
else:
return MetaArray(self._data.transpose(order), info=info)
except: except:
print(order) print(order)
raise raise
#### File I/O Routines #### File I/O Routines
def readFile(self, filename, **kwargs):
"""Load the data and meta info stored in *filename*"""
## decide which read function to use
fd = open(filename, 'rb')
magic = fd.read(8)
if magic == '\x89HDF\r\n\x1a\n':
fd.close()
self._readHDF5(filename, **kwargs)
self._isHDF = True
else:
fd.seek(0)
meta = MetaArray._readMeta(fd)
if 'version' in meta:
ver = meta['version']
else:
ver = 1
rFuncName = '_readData%s' % str(ver)
if not hasattr(MetaArray, rFuncName):
raise Exception("This MetaArray library does not support array version '%s'" % ver)
rFunc = getattr(self, rFuncName)
rFunc(fd, meta, **kwargs)
self._isHDF = False
@staticmethod @staticmethod
def _readMeta(fd): def _readMeta(fd):
@ -646,10 +710,8 @@ class MetaArray(np.ndarray):
#print ret #print ret
return ret return ret
@staticmethod def _readData1(self, fd, meta, mmap=False):
def _readData1(fd, meta, subtype, mmap=False): ## Read array data from the file descriptor for MetaArray v1 files
"""Read array data from the file descriptor for MetaArray v1 files
"""
## read in axis values for any axis that specifies a length ## read in axis values for any axis that specifies a length
frameSize = 1 frameSize = 1
for ax in meta['info']: for ax in meta['info']:
@ -664,12 +726,10 @@ class MetaArray(np.ndarray):
else: else:
subarr = np.fromstring(fd.read(), dtype=meta['type']) subarr = np.fromstring(fd.read(), dtype=meta['type'])
subarr.shape = meta['shape'] subarr.shape = meta['shape']
subarr = subarr.view(subtype) self._info = meta['info']
subarr._info = meta['info'] self._data = subarr
return subarr
@staticmethod def _readData2(self, fd, meta, mmap=False, subset=None):
def _readData2(fd, meta, subtype, mmap=False, subset=None):
## read in axis values ## read in axis values
dynAxis = None dynAxis = None
frameSize = 1 frameSize = 1
@ -768,13 +828,14 @@ class MetaArray(np.ndarray):
ax['values'] = np.array(xVals, dtype=ax['values_type']) ax['values'] = np.array(xVals, dtype=ax['values_type'])
del ax['values_len'] del ax['values_len']
del ax['values_type'] del ax['values_type']
subarr = subarr.view(subtype) #subarr = subarr.view(subtype)
subarr._info = meta['info'] #subarr._info = meta['info']
self._info = meta['info']
self._data = subarr
#raise Exception() ## stress-testing #raise Exception() ## stress-testing
return subarr #return subarr
@staticmethod def _readHDF5(self, fileName, close=False, writable=False):
def _readHDF5(fileName, subtype, mmap=False, writable=False):
if not HAVE_HDF5: if not HAVE_HDF5:
raise Exception("The file '%s' is HDF5-formatted, but the HDF5 library (h5py) was not found." % fileName) raise Exception("The file '%s' is HDF5-formatted, but the HDF5 library (h5py) was not found." % fileName)
f = h5py.File(fileName, 'r') f = h5py.File(fileName, 'r')
@ -782,16 +843,19 @@ class MetaArray(np.ndarray):
if ver > MetaArray.version: if ver > MetaArray.version:
print("Warning: This file was written with MetaArray version %s, but you are using version %s. (Will attempt to read anyway)" % (str(ver), str(MetaArray.version))) print("Warning: This file was written with MetaArray version %s, but you are using version %s. (Will attempt to read anyway)" % (str(ver), str(MetaArray.version)))
meta = MetaArray.readHDF5Meta(f['info']) meta = MetaArray.readHDF5Meta(f['info'])
self._info = meta
if mmap: if close:
arr = MetaArray.mapHDF5Array(f['data'], writable=writable) self._data = f['data'][:]
f.close()
else: else:
arr = f['data'][:] self._data = f['data']
self._openFile = f
#meta = H5MetaList(f['info']) #meta = H5MetaList(f['info'])
subarr = arr.view(subtype) #subarr = arr.view(subtype)
subarr._info = meta #subarr._info = meta
f.close() #self._data = arr
return subarr #return subarr
@staticmethod @staticmethod
def mapHDF5Array(data, writable=False): def mapHDF5Array(data, writable=False):