diff --git a/modules/base/pymod/table.py b/modules/base/pymod/table.py
index 2e5188ea15e3e3edc61072c60a6619fb2919fdeb..6eea1f01062c8bc8e744ba15f8f15f2926260102 100644
--- a/modules/base/pymod/table.py
+++ b/modules/base/pymod/table.py
@@ -134,7 +134,7 @@ class Table(object):
tab=Table()
If you want to add columns directly when creating the table, column names
- and column types can be specified as follows
+ and *column types* can be specified as follows
.. code-block:: python
@@ -144,6 +144,17 @@ class Table(object):
float and bool, respectively. There will be no data in the table and thus,
the table will not contain any rows.
+ The following *column types* are supported:
+
+ ======= ========
+ name abbrev
+ ======= ========
+ string s
+ float f
+ int i
+ bool b
+ ======= ========
+
If you want to add data to the table in addition, use the following:
.. code-block:: python
@@ -354,7 +365,7 @@ class Table(object):
def __str__(self):
return self.ToString()
- def _AddRowsFromDict(self, d, merge=False):
+ def _AddRowsFromDict(self, d, overwrite=False):
# get column indices
idxs = [self.GetColIndex(k) for k in d.keys()]
@@ -377,11 +388,11 @@ class Table(object):
new_row[idx] = self._Coerce(v, self.col_types[idx])
# partially overwrite existing row with new data
- if merge:
- merge_idx = self.GetColIndex(merge)
+ if overwrite:
+ overwrite_idx = self.GetColIndex(overwrite)
added = False
for i,r in enumerate(self.rows):
- if r[merge_idx]==new_row[merge_idx]:
+ if r[overwrite_idx]==new_row[overwrite_idx]:
for j,e in enumerate(self.rows[i]):
if new_row[j]==None:
new_row[j] = e
@@ -389,22 +400,30 @@ class Table(object):
added = True
break
- # if not merge or merge did not find appropriate row
- if not merge or not added:
+ # if not overwrite or overwrite did not find appropriate row
+ if not overwrite or not added:
self.rows.append(new_row)
- def AddRow(self, data, merge=None):
+ def AddRow(self, data, overwrite=None):
"""
- Add a row to the table. *row* may either a dictionary in which case the keys
- in the dictionary must match the column names. Columns not found in the dict
- will be initialized to None. Alternatively, if data is a list-like object,
- the row is initialized from the values in data. The number of items in data
- must match the number of columns in the table. A :class:`ValuerError` is
- raised otherwise.
+ Add a row to the table.
+
+ *row* may either be a dictionary or a list-like object.
+ In the case of a dictionary the keys in the dictionary must match the column
+ names. Columns not found in the dict will be initialized to None.
+ Alternatively, if data is a list-like object, the row is initialized from
+ the values in data. The number of items in data must match the number of
+ columns in the table. A :class:`ValuerError` is raised otherwise. The values
+ are added in the order specified in the list, thus, the order of the data
+ must match the columns.
+
+ If *overwrite* is set and not None (must be set to an existing column name),
+ an existing row is overwritten if the value of column *overwrite* matches.
+ If no matching row is found, a new row is appended to the table.
"""
if type(data)==dict:
- self._AddRowsFromDict(data, merge)
+ self._AddRowsFromDict(data, overwrite)
else:
if len(data)!=len(self.col_names):
msg='data array must have %d elements, not %d'
@@ -412,17 +431,17 @@ class Table(object):
new_row = [self._Coerce(v, t) for v, t in zip(data, self.col_types)]
# fully overwrite existing row with new data
- if merge:
- merge_idx = self.GetColIndex(merge)
+ if overwrite:
+ overwrite_idx = self.GetColIndex(overwrite)
added = False
for i,r in enumerate(self.rows):
- if r[merge_idx]==new_row[merge_idx]:
+ if r[overwrite_idx]==new_row[overwrite_idx]:
self.rows[i] = new_row
added = True
break
- # if not merge or merge did not find appropriate row
- if not merge or not added:
+ # if not overwrite or overwrite did not find appropriate row
+ if not overwrite or not added:
self.rows.append(new_row)
def RemoveCol(self, col):
@@ -584,9 +603,13 @@ class Table(object):
"""
Load table from stream or file with given name.
+ By default, the file format is *ost* (see below) and is *not* automatically
+ determined (e.g. from file extension). Thus, it *format* must be specified
+ for reading other file formats.
+
The following file formats are understood:
- ost
+ - ost
This is an ost-specific, but still human readable file format. The file
(stream) must start with header line of the form
@@ -599,11 +622,11 @@ class Table(object):
data items are automatically converted to the column format. Lines starting
with a '#' and empty lines are ignored.
- pickle
+ - pickle
Deserializes the table from a pickled byte stream
- csv
+ - csv
Reads the table from comma separated values stream. Since there is no
explicit type information in the csv file, the column types are guessed,
@@ -657,15 +680,15 @@ class Table(object):
"""
Allows to conveniently iterate over a selection of columns, e.g.
- .. code-block::python
+ .. code-block:: python
tab=Table.Load('...')
- for col1, col in tab.Zip('col1', 'col2'):
+ for col1, col2 in tab.Zip('col1', 'col2'):
print col1, col2
is a shortcut for
- .. code-block::python
+ .. code-block:: python
tab=Table.Load('...')
for col1, col2 in zip(tab['col1'], tab['col2']):
@@ -820,8 +843,8 @@ class Table(object):
histtype='stepfilled', align='mid', x_title=None,
y_title=None, title=None, clear=True, save=False):
"""
- Create a histogram of the data in col for the range x_range, split into
- num_bins bins and plot it using matplot lib
+ Create a histogram of the data in col for the range *x_range*, split into
+ *num_bins* bins and plot it using matplot lib.
"""
try:
import matplotlib.pyplot as plt
@@ -1158,17 +1181,18 @@ class Table(object):
raise
- def Save(self, stream, format='ost', sep=','):
+ def Save(self, stream_or_filename, format='ost', sep=','):
"""
- Save the table to stream or filename
+ Save the table to stream or filename. For supported file formats, see
+ :meth:`Load`
"""
format=format.lower()
if format=='ost':
- return self._SaveOST(stream)
+ return self._SaveOST(stream_or_filename)
if format=='csv':
- return self._SaveCSV(stream, sep=sep)
+ return self._SaveCSV(stream_or_filename, sep=sep)
if format=='pickle':
- return self._SavePickle(stream)
+ return self._SavePickle(stream_or_filename)
raise ValueError('unknown format "%s"' % format)
def _SavePickle(self, stream):
@@ -1317,7 +1341,9 @@ class Table(object):
style='-', title=None, x_title=None, y_title=None,
clear=True, save=None):
'''
- Plot an enrichment curve using matplotlib
+ Plot an enrichment curve using matplotlib.
+
+ For more information about parameters, see :meth:`ComputeEnrichment`
'''
try:
@@ -1417,7 +1443,9 @@ class Table(object):
class_dir='-', class_cutoff=2.0):
'''
Computes the area under the curve of the enrichment using the trapezoidal
- rule
+ rule.
+
+ For more information about parameters, see :meth:`ComputeEnrichment`
'''
try:
import numpy as np
@@ -1439,23 +1467,27 @@ class Table(object):
For this it is necessary, that the datapoints are classified into positive
and negative points. This can be done in two ways:
- - by using one 'bool' column (class_col) which contains True for positives
+ - by using one 'bool' column (*class_col*) which contains True for positives
and False for negatives
- - by using a non-bool column (class_col), a cutoff value (class_cutoff)
- and the classification columns direction (class_dir). This will generate
+ - by using a non-bool column (*class_col*), a cutoff value (*class_cutoff*)
+ and the classification columns direction (*class_dir*). This will generate
the classification on the fly
- * if class_dir=='-': values in the classification column that are
- less than or equal to class_cutoff will be counted
- as positives
- * if class_dir=='+': values in the classification column that are
- larger than or equal to class_cutoff will be counted
+ - if *class_dir* =='-': values in the classification column that are
+ less than or equal to *class_cutoff* will be counted
as positives
+ - if *class_dir* =='+': values in the classification column that are
+ larger than or equal to *class_cutoff* will be
+ counted as positives
- During the calculation, the table will be sorted according to score_dir,
+ During the calculation, the table will be sorted according to *score_dir*,
where a '-' values means smallest values first and therefore, the smaller
the value, the better.
+ If *class_col* does not contain any positives (i.e. value is True (if column
+ is of type bool) or evaluated to True (if column is of type int or float
+ (depending on *class_dir* and *class_cutoff*))) the ROC is not defined and
+ the function will return *None*.
'''
ALLOWED_DIR = ['+','-']
@@ -1516,7 +1548,9 @@ class Table(object):
class_dir='-', class_cutoff=2.0):
'''
Computes the area under the curve of the receiver operating characteristics
- using the trapezoidal rule
+ using the trapezoidal rule.
+
+ For more information about parameters, see :meth:`ComputeROC`
'''
try:
import numpy as np
@@ -1536,7 +1570,9 @@ class Table(object):
style='-', title=None, x_title=None, y_title=None,
clear=True, save=None):
'''
- Plot an ROC curve using matplotlib
+ Plot an ROC curve using matplotlib.
+
+ For more information about parameters, see :meth:`ComputeROC`
'''
try:
@@ -1612,6 +1648,43 @@ class Table(object):
return False
return True
+ def Extend(self, tab, overwrite=None):
+ """
+ Append each row of *tab* to the current table. The data is appended based
+ on the column names, thus the order of the table columns is *not* relevant,
+ only the header names.
+
+ If there is a column in *tab* that is not present in the current table,
+ it is added to the current table and filled with *None* for all the rows
+ present in the current table.
+
+ If the type of any column in *tab* is not the same as in the current table
+ a *TypeError* is raised.
+
+ If *overwrite* is set and not None (must be set to an existing column name),
+ an existing row is overwritten if the value of column *overwrite* matches.
+ If no matching row is found, a new row is appended to the table.
+ """
+ # add column to current table if it doesn't exist
+ for name,typ in zip(tab.col_names, tab.col_types):
+ if not name in self.col_names:
+ self.AddCol(name, typ)
+
+ # check that column types are the same in current and new table
+ for name in self.col_names:
+ curr_type = self.col_types[self.GetColIndex(name)]
+ new_type = tab.col_types[tab.GetColIndex(name)]
+ if curr_type!=new_type:
+ raise TypeError('cannot extend table, column %s in new '%name +\
+ 'table different type (%s) than in '%new_type +\
+ 'current table (%s)'%curr_type)
+
+ num_rows = len(tab.rows)
+ for i in range(0,num_rows):
+ row = tab.rows[i]
+ data = dict(zip(tab.col_names,row))
+ self.AddRow(data, overwrite)
+
def Merge(table1, table2, by, only_matching=False):
"""
diff --git a/modules/base/tests/test_table.py b/modules/base/tests/test_table.py
index 88a799dee114f5d5d2f9961d07707f74957faef5..ea823869c3e67cec719dce4b21794e005cb6f85e 100644
--- a/modules/base/tests/test_table.py
+++ b/modules/base/tests/test_table.py
@@ -62,9 +62,9 @@ class TestTable(unittest.TestCase):
self.CompareColCount(tab, 3)
self.CompareRowCount(tab, 0)
self.CompareColTypes(tab, ['first','second', 'third'], 'sif')
- tab.AddRow(['x',3, None], merge=None)
- tab.AddRow(['foo',None, 2.2], merge=None)
- tab.AddRow([None,9, 3.3], merge=None)
+ tab.AddRow(['x',3, None], overwrite=None)
+ tab.AddRow(['foo',None, 2.2], overwrite=None)
+ tab.AddRow([None,9, 3.3], overwrite=None)
return tab
def CompareRowCount(self, t, row_count):
@@ -375,7 +375,7 @@ class TestTable(unittest.TestCase):
tab = Table(['first'],'i')
self.CompareColCount(tab, 1)
self.CompareRowCount(tab, 0)
- tab.AddRow([2], merge=None)
+ tab.AddRow([2], overwrite=None)
self.CompareColCount(tab, 1)
self.CompareRowCount(tab, 1)
self.CompareColNames(tab, ['first'])
@@ -394,7 +394,7 @@ class TestTable(unittest.TestCase):
tab.AddCol('first', 'int')
self.CompareColCount(tab, 1)
self.CompareRowCount(tab, 0)
- tab.AddRow([2], merge=None)
+ tab.AddRow([2], overwrite=None)
self.CompareColCount(tab, 1)
self.CompareRowCount(tab, 1)
self.CompareColNames(tab, ['first'])
@@ -414,7 +414,7 @@ class TestTable(unittest.TestCase):
self.CompareColCount(tab, 2)
self.CompareRowCount(tab, 0)
self.CompareColTypes(tab, ['first','second'], 'si')
- tab.AddRow(['x',3], merge=None)
+ tab.AddRow(['x',3], overwrite=None)
self.CompareColCount(tab, 2)
self.CompareRowCount(tab, 1)
tab.AddCol('third', 'float', 3.141)
@@ -441,9 +441,9 @@ class TestTable(unittest.TestCase):
self.CompareColCount(tab, 3)
self.CompareRowCount(tab, 0)
self.CompareColTypes(tab, ['first','second', 'third'], 'sif')
- tab.AddRow(['x',3, 1.0], merge=None)
- tab.AddRow(['foo',6, 2.2], merge=None)
- tab.AddRow(['bar',9, 3.3], merge=None)
+ tab.AddRow(['x',3, 1.0], overwrite=None)
+ tab.AddRow(['foo',6, 2.2], overwrite=None)
+ tab.AddRow(['bar',9, 3.3], overwrite=None)
self.CompareColCount(tab, 3)
self.CompareRowCount(tab, 3)
self.CompareDataFromDict(tab, {'second': [3,6,9], 'first': ['x','foo','bar'], 'third': [1,2.2,3.3]})
@@ -466,9 +466,9 @@ class TestTable(unittest.TestCase):
self.CompareColCount(tab, 3)
self.CompareRowCount(tab, 0)
self.CompareColTypes(tab, ['first','second', 'aaa'], 'sif')
- tab.AddRow({'first':'x','second':3, 'aaa':1.0}, merge=None)
- tab.AddRow({'aaa':2.2, 'second':6, 'first':'foo'}, merge=None)
- tab.AddRow({'second':9, 'aaa':3.3, 'first':'bar'}, merge=None)
+ tab.AddRow({'first':'x','second':3, 'aaa':1.0}, overwrite=None)
+ tab.AddRow({'aaa':2.2, 'second':6, 'first':'foo'}, overwrite=None)
+ tab.AddRow({'second':9, 'aaa':3.3, 'first':'bar'}, overwrite=None)
self.CompareColCount(tab, 3)
self.CompareRowCount(tab, 3)
self.CompareDataFromDict(tab, {'second': [3,6,9], 'first': ['x','foo','bar'], 'aaa': [1,2.2,3.3]})
@@ -490,9 +490,9 @@ class TestTable(unittest.TestCase):
self.CompareColCount(tab, 1)
self.CompareRowCount(tab, 0)
self.CompareColTypes(tab, ['first'], 's')
- tab.AddRow(['x'], merge=None)
- tab.AddRow(['foo'], merge=None)
- tab.AddRow(['bar'], merge=None)
+ tab.AddRow(['x'], overwrite=None)
+ tab.AddRow(['foo'], overwrite=None)
+ tab.AddRow(['bar'], overwrite=None)
tab.AddCol('second', 'int')
tab.AddCol('third', 'float', 3.141)
self.CompareColCount(tab, 3)
@@ -501,9 +501,9 @@ class TestTable(unittest.TestCase):
'first': ['x','foo','bar'],
'third': [3.141, 3.141, 3.141]})
- def testAddRowFromDictWithMerge(self):
+ def testAddRowFromDictWithOverwrite(self):
'''
- add rows from dictionary with merge (i.e. overwrite third row with additional data)
+ add rows from dictionary with overwrite (i.e. overwrite third row with additional data)
x foo bar
------------------
@@ -522,14 +522,14 @@ class TestTable(unittest.TestCase):
self.CompareDataFromDict(tab, {'x': ['row1', 'row2', 'row3'],
'foo': [True, None, False],
'bar': [1, 2, None]})
- tab.AddRow({'x':'row3', 'bar':3}, merge='x')
+ tab.AddRow({'x':'row3', 'bar':3}, overwrite='x')
self.CompareDataFromDict(tab, {'x': ['row1', 'row2', 'row3'],
'foo': [True, None, False],
'bar': [1, 2, 3]})
- def testAddRowFromListWithMerge(self):
+ def testAddRowFromListWithOverwrite(self):
'''
- add rows from list with merge (i.e. overwrite third row with additional data)
+ add rows from list with overwrite (i.e. overwrite third row with additional data)
x foo bar
------------------
@@ -549,7 +549,7 @@ class TestTable(unittest.TestCase):
self.CompareDataFromDict(tab, {'x': ['row1', 'row2', 'row3'],
'foo': [True, None, False],
'bar': [1, 2, None]})
- tab.AddRow(['row3', True, 3], merge='x')
+ tab.AddRow(['row3', True, 3], overwrite='x')
self.CompareDataFromDict(tab, {'x': ['row1', 'row2', 'row3'],
'foo': [True, None, True],
'bar': [1, 2, 3]})
@@ -1288,6 +1288,101 @@ class TestTable(unittest.TestCase):
tab.AddRow([None,8, 2])
self.assertAlmostEquals(tab.SpearmanCorrel('second','third'), -0.316227766)
+ def testExtend(self):
+ '''
+ first second third
+ ----------------------
+ x 3 NA
+ foo NA 2.200
+ NA 9 3.300
+ '''
+
+ # simple extend of the same table
+ tab = self.CreateTestTable()
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None],
+ 'second': [3,None,9],
+ 'third': [None,2.2,3.3]})
+
+ tab.Extend(tab)
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None,'x','foo',None],
+ 'second': [3,None,9,3,None,9],
+ 'third': [None,2.2,3.3,None,2.2,3.3]})
+
+ # simple extend of different tables with the same data
+ tab = self.CreateTestTable()
+ tab2 = self.CreateTestTable()
+ tab.Extend(tab2)
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None,'x','foo',None],
+ 'second': [3,None,9,3,None,9],
+ 'third': [None,2.2,3.3,None,2.2,3.3]})
+ self.CompareDataFromDict(tab2, {'first': ['x','foo',None],
+ 'second': [3,None,9],
+ 'third': [None,2.2,3.3]})
+
+ # add additional columns to current table
+ tab = self.CreateTestTable()
+ tab2 = self.CreateTestTable()
+ tab2.AddCol('foo','i',[1,2,3])
+ tab.Extend(tab2)
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None,'x','foo',None],
+ 'second': [3,None,9,3,None,9],
+ 'third': [None,2.2,3.3,None,2.2,3.3],
+ 'foo': [None,None,None,1,2,3]})
+
+ # different order of the data
+ tab = self.CreateTestTable()
+ tab2 = Table(['third','second','first'],
+ 'fis',
+ third=[None,2.2,3.3],
+ first=['x','foo',None],
+ second=[3, None, 9])
+ self.CompareDataFromDict(tab2, {'first': ['x','foo',None],
+ 'second': [3,None,9],
+ 'third': [None,2.2,3.3]})
+ tab.Extend(tab2)
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None,'x','foo',None],
+ 'second': [3,None,9,3,None,9],
+ 'third': [None,2.2,3.3,None,2.2,3.3]})
+
+ # with overwrite (additional column)
+ tab = self.CreateTestTable()
+ tab2 = self.CreateTestTable()
+ tab2.AddCol('foo','i',[1,2,3])
+ tab.Extend(tab2, overwrite='first')
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None],
+ 'second': [3,None,9],
+ 'third': [None,2.2,3.3],
+ 'foo': [1,2,3]})
+
+ # with overwrite (no matching value)
+ tab = self.CreateTestTable()
+ tab2 = Table(['third','second','first'],
+ 'fis',
+ third=[None,2.2,3.3],
+ first=['a','bar','bla'],
+ second=[3, None, 9])
+ tab.Extend(tab2, overwrite='first')
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None,'a','bar','bla'],
+ 'second': [3,None,9,3,None,9],
+ 'third': [None,2.2,3.3,None,2.2,3.3]})
+
+ # with overwrite (with matching values)
+ tab = self.CreateTestTable()
+ tab2 = Table(['third','second','first'],
+ 'fis',
+ third=[None,2.2,3.4],
+ first=['a','bar','bla'],
+ second=[3, None, 9])
+ tab.Extend(tab2, overwrite='third')
+ self.CompareDataFromDict(tab, {'first': ['a','bar',None,'bla'],
+ 'second': [3,None,9,9],
+ 'third': [None,2.2,3.3,3.4]})
+
+ # cannot extend if types are different
+ tab = Table('aaa','s',a=['a','b'])
+ tab2 = Table('aaa','i',a=[1,2])
+ self.assertRaises(TypeError, tab.Extend, tab2)
+
if __name__ == "__main__":
from ost import testutils
testutils.RunTests()
diff --git a/modules/io/src/img/map_io_spi_handler.cc b/modules/io/src/img/map_io_spi_handler.cc
index d22897f4ee3976555418d3fdd8c0f49f49a14aa7..6f5e1798b4674ed037884719036eeeda30323f6e 100644
--- a/modules/io/src/img/map_io_spi_handler.cc
+++ b/modules/io/src/img/map_io_spi_handler.cc
@@ -198,9 +198,6 @@ void prep_header(spider_header& header, const img::Size& size, const geom::Vec3&
header.fNcol = ncol;
header.fLenbyt = ncol*4.0; // record length in bytesS
header.fLabrec = ceil(1024.0 / header.fLenbyt); // nr label records in file header
- if (fmod(1024,header.fLenbyt) != 0.0) {
- header.fLabrec += 1.0;
- }
header.fLabbyt = header.fLabrec * header.fLenbyt;
header.fIangle = 0.0; // flag indicating that tilt angles have been filled
header.fScale = spatial_sampling; // scale
@@ -389,6 +386,10 @@ void real_filler(std::istream& in, const spider_header& header, img::ImageHandle
template <typename B >
void real_dumper(std::ostream& f, const spider_header& header, const img::ImageHandle& mh,const img::alg::Normalizer& norm, bool swap_flag)
{
+ int padding = header.fLabbyt-f.tellp();
+ char* buffer=new char[padding];
+ f.write(buffer,padding);
+ delete[] buffer;
int slice_size=static_cast<int>(header.fNcol) * static_cast<int>(header.fNrow);
boost::scoped_array<B> rawp(new B[slice_size]);
diff --git a/modules/io/src/img/map_io_tiff_handler.cc b/modules/io/src/img/map_io_tiff_handler.cc
index b1050724393b5ddf5bf3677af351125f61ef2d4b..0f418bc896c6f0563a5a3a0d38d1e5aecfe6495e 100644
--- a/modules/io/src/img/map_io_tiff_handler.cc
+++ b/modules/io/src/img/map_io_tiff_handler.cc
@@ -311,7 +311,7 @@ void MapIOTiffHandler::do_export(const img::MapHandle& image,TIFF* tfile,TIF& fo
img::Point ori=image.GetSpatialOrigin();
geom::Vec3 sampling=image.GetPixelSampling();
float xreso=sampling[0]/Units::cm,yreso=sampling[1]/Units::cm;
- float xpos=xreso*ori[0],ypos=yreso*ori[1];
+ float xpos=std::max<Real>(0.0,xreso*ori[0]),ypos=std::max<Real>(0.0,yreso*ori[1]); //tiff file format only allows positivie origins, negative origins are lost here
TIFFSetField(tfile,TIFFTAG_IMAGEWIDTH,width);
TIFFSetField(tfile,TIFFTAG_IMAGELENGTH,height);
TIFFSetField(tfile,TIFFTAG_SAMPLESPERPIXEL,spp);
diff --git a/modules/io/tests/test_io_img.cc b/modules/io/tests/test_io_img.cc
index d9116842a780e8870192ba941b06703f04f417fa..890a7a9c29a22beb57b4c7c0aa0ffb04273f8777 100644
--- a/modules/io/tests/test_io_img.cc
+++ b/modules/io/tests/test_io_img.cc
@@ -47,7 +47,7 @@ BOOST_AUTO_TEST_CASE(test_io_img)
{
//float tests
boost::test_tools::close_at_tolerance<Real> close_test(::boost::test_tools::percent_tolerance(0.001));
- ost::img::ImageHandle testimage=ost::img::CreateImage(ost::img::Extent(ost::img::Point(0,0),ost::img::Point(3,3)));
+ ost::img::ImageHandle testimage=ost::img::CreateImage(ost::img::Extent(ost::img::Point(0,0),ost::img::Point(4,3)));
int counter=0;
for (img::ExtentIterator i(testimage.GetExtent()); !i.AtEnd(); ++i, ++counter) {
testimage.SetReal(i, counter);
@@ -57,7 +57,6 @@ BOOST_AUTO_TEST_CASE(test_io_img)
std::map<String,ImageFormatBase*> float_formats;
float_formats["DX"]=new DX;
float_formats["Situs"]=new Situs;
- float_formats["DAT (float)"]=new DAT(false,OST_FLOAT_FORMAT);
float_formats["CCP4 (float)"]=new MRC;
float_formats["MRC (float)"]=new MRC(false,MRC_OLD_FORMAT);
float_formats["SPIDER"]= new Spider;
@@ -84,7 +83,6 @@ BOOST_AUTO_TEST_CASE(test_io_img)
//int 16 formats
std::map<String,ImageFormatBase*> int_formats;
int_formats["IPL (16 bit)"]=new IPL(true,OST_BIT16_FORMAT);
- int_formats["DAT (16 bit)"]=new DAT(true,OST_BIT16_FORMAT);
int_formats["TIF (16 bit)"]=new TIF;
int_formats["JPK (16 bit)"]=new JPK;
// int_formats["DF3"]=new DF3(true);
@@ -137,7 +135,6 @@ BOOST_AUTO_TEST_CASE(test_io_img)
//byte formats
std::map<String,ImageFormatBase*> byte_formats;
- byte_formats["DAT (byte)"]=new DAT(true,OST_BIT8_FORMAT);
byte_formats["PNG"]=new PNG;
byte_formats["JPK (byte)"]= new JPK(true,OST_BIT8_FORMAT);
byte_formats["TIF (byte)"]= new TIF(true,OST_BIT8_FORMAT);
@@ -161,4 +158,70 @@ BOOST_AUTO_TEST_CASE(test_io_img)
}
}
+BOOST_AUTO_TEST_CASE(test_io_img_dat)
+{
+ // test for the dat file format using a square image (non square images not supported by dat)
+ //float test
+ boost::test_tools::close_at_tolerance<Real> close_test(::boost::test_tools::percent_tolerance(0.001));
+ ost::img::ImageHandle testimage=ost::img::CreateImage(ost::img::Extent(ost::img::Point(0,0),ost::img::Point(3,3)));
+ int counter=0;
+ for (img::ExtentIterator i(testimage.GetExtent()); !i.AtEnd(); ++i, ++counter) {
+ testimage.SetReal(i, counter);
+ }
+ testimage+=5.01; //if all values are > 0.0 we can use close_at_tolerance
+ const String fname("temp_img.tmp");
+ ost::io::SaveImage(testimage,fname,DAT(false,OST_FLOAT_FORMAT));
+ ost::img::ImageHandle loadedimage=ost::io::LoadImage(fname,DAT(false,OST_FLOAT_FORMAT));
+ bool failed=false;
+ ost::img::ExtentIterator eit(testimage.GetExtent());
+ for(;!eit.AtEnd();++eit) {
+ if( ! close_test(testimage.GetReal(eit),loadedimage.GetReal(eit))){
+ failed=true;
+ break;
+ }
+ }
+ if(failed){
+ BOOST_ERROR("Image IO failed for plugin DAT (float) at point " << ost::img::Point(eit)<< ". The values are: " << testimage.GetReal(eit)<< ","<< loadedimage.GetReal(eit) );
+ }
+ //int 16 format
+ ost::io::SaveImage(testimage,fname,DAT(true,OST_BIT16_FORMAT));
+ loadedimage=ost::io::LoadImage(fname,DAT(true,OST_BIT16_FORMAT));
+ ost::img::alg::Normalizer norm=ost::img::alg::CreateLinearRangeNormalizer(testimage,0.0,65535.0);
+ ost::img::ImageHandle scaled_image=testimage.Apply(norm);
+ failed=false;
+ eit=ost::img::ExtentIterator(testimage.GetExtent());
+ for(;!eit.AtEnd();++eit) {
+ if( static_cast<int>(scaled_image.GetReal(eit))!=static_cast<int>(loadedimage.GetReal(eit))){
+ failed=true;
+ break;
+ }
+ }
+ if(failed){
+ BOOST_ERROR("Image IO failed for plugin DAT (int16) at point "
+ << ost::img::Point(eit)<< ". Should be "
+ << static_cast<int>(scaled_image.GetReal(eit)) << ", but "
+ << static_cast<int>(loadedimage.GetReal(eit)) << " found.");
+ }
+
+ //byte format
+ ost::io::SaveImage(testimage,fname,DAT(true,OST_BIT8_FORMAT));
+ loadedimage=ost::io::LoadImage(fname,DAT(true,OST_BIT8_FORMAT));
+ norm=ost::img::alg::CreateLinearRangeNormalizer(testimage,0.0,255.0);
+ scaled_image=testimage.Apply(norm);
+ failed=false;
+ eit=ost::img::ExtentIterator(testimage.GetExtent());
+ for(;!eit.AtEnd();++eit) {
+ if( static_cast<int>(scaled_image.GetReal(eit))!=static_cast<int>(loadedimage.GetReal(eit))){
+ failed=true;
+ break;
+ }
+ }
+ if(failed){
+ BOOST_ERROR("Image IO failed for plugin DAT (int8) at point "
+ << ost::img::Point(eit)<< ". Should be "
+ << static_cast<int>(scaled_image.GetReal(eit)) << ", but "
+ << static_cast<int>(loadedimage.GetReal(eit)) << " found.");
+ }
+}
+
BOOST_AUTO_TEST_SUITE_END()