diff --git a/pyglance/glance/data.py b/pyglance/glance/data.py
index fe407d66b04665ecca99c809339d2b26150ea300..af8e40591da7b19375260b2c5ce994d5b6f1aabc 100644
--- a/pyglance/glance/data.py
+++ b/pyglance/glance/data.py
@@ -237,14 +237,36 @@ class DiffInfoObject (object) :
(if both a value and percent are present, two epsilon tests will be done)
"""
- # Upcasts to be used in difference computation to avoid overflow. Currently only unsigned
- # ints are upcast.
- # FUTURE: handle uint64s as well (there is no int128, so might have to detect overflow)
+ POSITIVE_UPCASTS = {
+ np.uint8: np.int16,
+ np.uint16: np.int32,
+ np.uint32: np.int64,
+ np.uint64: np.float32,
+ }
+
+ # Upcasts to be used in difference computation to avoid overflow.
+ # right now this is agressively upcasting the comparison data
DATATYPE_UPCASTS = {
- np.uint8: np.int16,
- np.uint16: np.int32,
- np.uint32: np.int64
- }
+ np.int8: np.int16,
+ np.int16: np.int32,
+ np.int32: np.int64,
+ np.int64: np.float32,
+
+ #np.float32: np.float64,
+ #np.float64: np.float128,
+ }
+ # FUTURE: right now the actual range of the data isn't being considered when upcasting
+ # (Note: numpy.finfo and numpy.iinfo can be used to get more data on types)
+ TYPE_MAXIMUM = {
+ np.int16: 32767,
+ np.int32: 2147483647,
+ np.int64: 9223372036854775807,
+
+ np.float32: 3.4028235e+38,
+
+ np.float64: 1.7976931348623157e+308,
+ #np.float128: 1.189731495357231765e+4932,
+ }
def __init__(self, aDataObject, bDataObject,
epsilonValue=0.0, epsilonPercent=None) :
@@ -278,9 +300,17 @@ class DiffInfoObject (object) :
type_to_return = np.common_type(data1, data2)
changed_type = True
- # upcast the type if we need to
+ # make sure we're using a type that has negative values in it
+ if type_to_return in DiffInfoObject.POSITIVE_UPCASTS :
+ type_to_return = DiffInfoObject.POSITIVE_UPCASTS[type_to_return]
+ changed_type = True
+
+ # upcast the type if we think we'll need more space for subtracting
if type_to_return in DiffInfoObject.DATATYPE_UPCASTS :
type_to_return = DiffInfoObject.DATATYPE_UPCASTS[type_to_return]
+ changed_type = True
+
+ if changed_type :
LOG.debug('To prevent overflow, difference data will be upcast from ('
+ str(data1.dtype) + '/' + str(data2.dtype) + ') to: ' + str(type_to_return))
diff --git a/pyglance/glance/io.py b/pyglance/glance/io.py
index cbe5223c28ce60ca2759bef167bbbdc07f1ecf6c..55873ddf59245d1bc654dfdbced6471a61f98e3a 100644
--- a/pyglance/glance/io.py
+++ b/pyglance/glance/io.py
@@ -52,6 +52,13 @@ except ImportError:
LOG.info('no adl_blob format handler available')
adl_blob = None
+try :
+ from osgeo import gdal
+ LOG.info('loading osgeo module for GeoTIFF data file access')
+except :
+ LOG.info('no osgeo available for reading GeoTIFF data files')
+ gdal = None
+
UNITS_CONSTANT = "units"
fillValConst1 = '_FillValue'
@@ -916,6 +923,174 @@ class aeri(object):
# handle the variety of file suffixes by building aliases to aeri class
cxs = rnc = cxv = csv = spc = sum = uvs = aeri
+class tiff (object):
+ """wrapper for to open GeoTIFF data sets for comparison
+ __call__ yields sequence of variable names
+ __getitem__ returns individual variables ready for slicing to numpy arrays
+ """
+
+ _tiff = None
+
+ # if we are using meaningful names, we will translate between
+ # the band index numbers and these names (otherwise bands use generic names)
+ EXPECTED_BAND_NAME_KEY = {
+ 1: ["grayscale value"],
+ 3: ["red", "green", "blue"],
+ 4: ["red", "green", "blue", "alpha"],
+ }
+ SPECIAL_NAMES_TO_IDX = {
+ "grayscale value": 1,
+ "red": 1,
+ "green": 2,
+ "blue": 3,
+ "alpha": 4,
+ }
+
+ def _get_generic_band_name (self, number) :
+ """get a generic band name for this number"""
+
+ return ("band at index " + str(number))
+
+ def _get_band_index_from_name (self, name) :
+ """get an index for the band from a name
+
+ name may be either a meaningful name from the list that shows
+ up in SPECIAL_NAMES_TO_IDX's keys or a generic name that was
+ generated by _get_generic_band_name
+ """
+
+ to_return = None
+
+ if name in self.SPECIAL_NAMES_TO_IDX.keys() :
+ to_return = self.SPECIAL_NAMES_TO_IDX[name]
+ else :
+ to_return = int(name.split(' ')[-1])
+
+ return to_return
+
+ def __init__(self, filename, allowWrite=False, useMeaningfulNames=True):
+
+ if gdal is None:
+ LOG.error('gdal is not installed and is needed in order to read GeoTIFF files')
+ assert(gdal is not None)
+
+ if allowWrite:
+ LOG.warn("Write access requested, but is not currently supported for GeoTIFF files. File will be opened read-only.")
+
+ self._tiff = gdal.Open(filename)
+ self.niceNames = useMeaningfulNames
+
+ def __call__(self):
+ "yield names of variables to be compared"
+
+ # GeoTIFF files don't actually have named variables, so get something appropriate based on the numbering of bands
+ num_bands = self._tiff.RasterCount
+
+ to_return = [ ]
+ if self.niceNames and (num_bands in self.EXPECTED_BAND_NAME_KEY.keys()) :
+ to_return = self.EXPECTED_BAND_NAME_KEY[num_bands][:]
+ else :
+ for bandNumber in range(1, num_bands + 1) :
+ to_return.append(self._get_generic_band_name(bandNumber))
+
+ return to_return
+
+ # this returns a numpy array with a copy of the full, scaled
+ # data for this variable, if the data type must be changed to allow
+ # for scaling it will be (so the return type may not reflect the
+ # type found in the original file)
+ def __getitem__(self, name):
+
+ LOG.debug("opening variable: " + name)
+
+ # first figure out the index for this variable
+ var_index = self._get_band_index_from_name(name)
+
+ # get the data out of the file
+ temp_band = self._tiff.GetRasterBand(var_index)
+ temp_data = temp_band.ReadAsArray()
+
+ # there is no standard scaling procedure for GeoTIFFs, so skip that!
+
+ return temp_data
+
+ # TODO, this hasn't been supported in other file types
+ def close (self) :
+ # Dave couldn't find any explicit way to close it other
+ # than let the garbage collector take care of it
+ self._tiff = None
+
+ def get_variable_object(self, name):
+ return None
+
+ def missing_value(self, name):
+ return None
+
+ def create_new_variable(self, variablename, missingvalue=None, data=None, variabletocopyattributesfrom=None):
+ """
+ TODO, this is not yet supported for GeoTIFFs
+
+ create a new variable with the given name
+ optionally set the missing value (fill value) and data to those given
+
+ the created variable will be returned, or None if a variable could not
+ be created
+ """
+
+ LOG.warn ("GeoTIFF io class does not yet support writing. Unable to create new variable in GeoTIFF file.")
+
+ return None
+
+ def add_attribute_data_to_variable(self, variableName, newAttributeName, newAttributeValue) :
+ """
+ TODO this is not yet supported for GeoTIFFs
+
+ if the attribute exists for the given variable, set it to the new value
+ if the attribute does not exist for the given variable, create it and set it to the new value
+ """
+
+ LOG.warn ("GeoTIFF io class does not yet support writing. Unable to add attribute information to GeoTIFF file.")
+
+ return
+
+ def get_variable_attributes (self, variableName, caseInsensitive=True) :
+ """
+ returns all the attributes associated with a variable name
+ """
+
+ # FUTURE, GeoTIFF files do have attributes, but this isn't hooked up yet
+
+ return { }
+
+ def get_attribute(self, variableName, attributeName, caseInsensitive=True) :
+ """
+ returns the value of the attribute if it is available for this variable, or None
+ """
+
+ # FUTURE, GeoTIFF files do have attributes, but this isn't hooked up yet
+
+ return None
+
+ def get_global_attributes(self, caseInsensitive=True) :
+ """
+ get a list of all the global attributes for this file or None
+ """
+
+ # FUTURE, GeoTIFF files do have attributes, but this isn't hooked up yet
+
+ return { }
+
+ def get_global_attribute(self, attributeName, caseInsensitive=True) :
+ """
+ returns the value of a global attribute if it is available or None
+ """
+
+ # FUTURE, GeoTIFF files do have attributes, but this isn't hooked up yet
+
+ return None
+
+# people also name tiff files with one f...
+tif = tiff
def _search_xml(pathname):
xs = '.xml'
diff --git a/pyglance/glance/load.py b/pyglance/glance/load.py
index 034d37af541b50dd9bf0f382cb3a76a460897741..e35ba4167b76d368909523a0c8578bbec12ee12d 100644
--- a/pyglance/glance/load.py
+++ b/pyglance/glance/load.py
@@ -9,7 +9,7 @@ Copyright (c) 2012 University of Wisconsin SSEC. All rights reserved.
"""
import logging
-from pycdf import CDFError
+#from pycdf import CDFError
import numpy
import glance.delta as delta
@@ -249,10 +249,11 @@ def load_variable_data(fileObject, variableNameInFile,
else :
try :
variableData = numpy.array(fileObject[variableNameInFile]) if forceDType is None else numpy.array(fileObject[variableNameInFile], dtype=forceDType)
- except CDFError :
+ except Exception, ex :
+ import traceback
exceptionToRaise = ValueError('Unable to retrieve ' + variableNameInFile + ' data. The variable name ' +
' may not exist in this file or an error may have occured while attempting to' +
- ' access the data. Details of file access error observed: ' + str(CDFError))
+ ' access the data. Details of file access error observed: ' + str(ex))
# if we ended up with an exception, raise that now
if exceptionToRaise is not None :