def __init__(self, filename):
self._dbName = filename
db = SqliteDb()
db._createConnection(filename, 1000)
# Tables should be at pairs:
# PREFIX_Classes
# PREFIX_Objects
# where PREFIX can be empty
self.tablePrefixes = OrderedDict()
tables = db.getTables()
for t in tables:
if t.endswith('Classes'):
prefix = t.replace('Classes', '')
to = prefix + 'Objects'
if to not in tables:
raise Exception('SqliteDataSet: table "%s" found, but not "%s"' % (t, to))
flatDb = SqliteFlatDb(filename, tablePrefix=prefix)
tableName = prefix + self._getPlural(flatDb.getSelfClassName())
self.tablePrefixes[tableName] = prefix
#tablePrefixes.append(prefix)
DataSet.__init__(self, self.tablePrefixes.keys())
db.close()
def __init__(self, filename):
self._dbName = filename
db = SqliteDb()
db._createConnection(filename, 1000)
# Tables should be at pairs:
# PREFIX_Classes
# PREFIX_Objects
# where PREFIX can be empty
self.tablePrefixes = OrderedDict()
tables = db.getTables()
for t in tables:
if t.endswith('Classes'):
prefix = t.replace('Classes', '')
to = prefix + 'Objects'
if to not in tables:
raise Exception('SqliteDataSet: table "%s" found, but not "%s"' % (t, to))
flatDb = SqliteFlatDb(filename, tablePrefix=prefix)
tableName = prefix + self._getPlural(flatDb.getSelfClassName())
self.tablePrefixes[tableName] = prefix
#tablePrefixes.append(prefix)
DataSet.__init__(self, self.tablePrefixes.keys())
db.close()
def _loadTable(self, tableName):
""" Load information from tables PREFIX_Classes, PREFIX_Objects. """
tableName = self.tablePrefixes[tableName]
BASIC_COLUMNS = [
Column('id', int, renderType=COL_RENDER_ID),
Column('enabled', bool, renderType=COL_RENDER_CHECKBOX),
Column('label', str),
Column('comment', str),
Column('creation', str)
]
# Load columns from PREFIX_Classes table
columns = list(BASIC_COLUMNS)
db = SqliteDb()
db._createConnection(self._dbName, 1000)
db.executeCommand("SELECT * FROM %sClasses;" % tableName)
# This will store the images columsn to join
# the _index and the _filename
imgCols = {}
for row in db._iterResults():
renderType = COL_RENDER_NONE
colName = row['column_name']
colLabel = row['label_property']
if colLabel != 'self':
# Keep track of _index and _filename pairs to mark as renderable images
if colLabel.endswith('_index'):
imgCols[colLabel.replace('_index', '')] = colName
elif colLabel.endswith('_filename'):
# TODO: Maybe not all the labels endswith "_filename"
# have to be rendered.
# for example in the RotSpectra with '_representative._filename'
prefix = colLabel.replace('_filename', '')
if prefix in imgCols:
renderType = COL_RENDER_IMAGE
imgCols[colName] = imgCols[prefix]
#CTF FIX
elif (colLabel.endswith('_psdFile')
or colLabel.endswith('_enhanced_psd')
or colLabel.endswith('_ctfmodel_quadrant')
or colLabel.endswith('_ctfmodel_halfplane')):
renderType = COL_RENDER_IMAGE
if row['class_name'] == 'Boolean':
renderType = COL_RENDER_CHECKBOX
columns.append(
Column(colName, str, label=colLabel,
renderType=renderType))
table = Table(*columns)
checkedImgCols = {} # Check if the image columns are volumes
ih = ImageHandler()
# Populate the table in the DataSet
db.executeCommand("SELECT * FROM %sObjects;" % tableName)
for row in db._iterResults():
rowDict = dict(row)
for k, v in rowDict.iteritems():
if v is None:
rowDict[k] = ''
# Set the index@filename for images columns values
if k in imgCols:
colName = imgCols[k]
index = rowDict[colName]
filename = os.path.join(self.projectPath, rowDict[k])
filepath = filename.replace(":mrc", "")
if not checkedImgCols.get(colName, False):
if os.path.exists(filepath):
#print "Fn to get dims: %s@%s" % (index,filename)
x, y, z, n = ih.getDimensions((index, filename))
if z > 1:
table.getColumn(k).setRenderType(
COL_RENDER_VOLUME)
checkedImgCols[colName] = True
if index:
rowDict[k] = '%06d@%s' % (index, filename)
table.addRow(row['id'], **rowDict)
return table
def _loadTable(self, tableName):
""" Load information from tables PREFIX_Classes, PREFIX_Objects. """
tableName = self.tablePrefixes[tableName]
BASIC_COLUMNS = [Column('id', int, renderType=COL_RENDER_ID),
Column('enabled', bool ,renderType=COL_RENDER_CHECKBOX),
Column('label', str),
Column('comment', str),
Column('creation', str)]
# Load columns from PREFIX_Classes table
columns = list(BASIC_COLUMNS)
db = SqliteDb()
db._createConnection(self._dbName, 1000)
db.executeCommand("SELECT * FROM %sClasses;" % tableName)
# This will store the images columsn to join
# the _index and the _filename
imgCols = {}
for row in db._iterResults():
renderType = COL_RENDER_NONE
colName = row['column_name']
colLabel = row['label_property']
if colLabel != 'self':
# Keep track of _index and _filename pairs to mark as renderable images
if colLabel.endswith('_index'):
imgCols[colLabel.replace('_index', '')] = colName
elif colLabel.endswith('_filename'):
# TODO: Maybe not all the labels endswith "_filename"
# have to be rendered.
# for example in the RotSpectra with '_representative._filename'
prefix = colLabel.replace('_filename', '')
if prefix in imgCols:
renderType = COL_RENDER_IMAGE
imgCols[colName] = imgCols[prefix]
#CTF FIX
elif (colLabel.endswith('_psdFile') or
colLabel.endswith('_enhanced_psd') or
colLabel.endswith('_ctfmodel_quadrant') or
colLabel.endswith('_ctfmodel_halfplane')):
renderType = COL_RENDER_IMAGE
if row['class_name'] == 'Boolean':
renderType = COL_RENDER_CHECKBOX
columns.append(Column(colName, str, label=colLabel, renderType=renderType))
table = Table(*columns)
checkedImgCols = {} # Check if the image columns are volumes
ih = ImageHandler()
# Populate the table in the DataSet
db.executeCommand("SELECT * FROM %sObjects;" % tableName)
for row in db._iterResults():
rowDict = dict(row)
for k, v in rowDict.iteritems():
if v is None:
rowDict[k] = ''
# Set the index@filename for images columns values
if k in imgCols:
colName = imgCols[k]
index = rowDict[colName]
filename = os.path.join(self.projectPath, rowDict[k])
filepath = filename.replace(":mrc", "")
if not checkedImgCols.get(colName, False):
if os.path.exists(filepath):
#print "Fn to get dims: %s@%s" % (index,filename)
x, y, z, n = ih.getDimensions((index, filename))
if z > 1:
table.getColumn(k).setRenderType(COL_RENDER_VOLUME)
checkedImgCols[colName] = True
if index:
rowDict[k] = '%06d@%s' % (index, filename)
table.addRow(row['id'], **rowDict)
return table