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dwifslpreproc: Handle non-ascii data in eddy error outputs #2313

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May 6, 2021
Merged

dwifslpreproc: Handle non-ascii data in eddy error outputs #2313

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b4f18a3
dwifslpreproc: Handle non-ascii data in eddy error outputs
Lestropie May 6, 2021
f02940e
replace use of deprecated uint16/32 with uint16/32_t
jdtournier May 6, 2021
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4 changes: 2 additions & 2 deletions bin/dwifslpreproc
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Original file line number Diff line number Diff line change
Expand Up @@ -912,13 +912,13 @@ def execute(): #pylint: disable=unused-variable
except run.MRtrixCmdError as exception_cuda:
if not eddy_openmp_cmd:
raise
with open('eddy_cuda_failure_output.txt', 'w') as eddy_output_file:
with open('eddy_cuda_failure_output.txt', 'wb') as eddy_output_file:
eddy_output_file.write(str(exception_cuda))
app.console('CUDA version of \'eddy\' was not successful; attempting OpenMP version')
try:
eddy_output = run.command(eddy_openmp_cmd + ' ' + eddy_all_options)
except run.MRtrixCmdError as exception_openmp:
with open('eddy_openmp_failure_output.txt', 'w') as eddy_output_file:
with open('eddy_openmp_failure_output.txt', 'wb') as eddy_output_file:
eddy_output_file.write(str(exception_openmp))
# Both have failed; want to combine error messages
eddy_cuda_header = ('=' * len(eddy_cuda_cmd)) \
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12 changes: 6 additions & 6 deletions core/formats/tiff.cpp
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Expand Up @@ -35,13 +35,13 @@ namespace MR
if (! (Path::has_suffix (H.name(), ".tiff") ||
Path::has_suffix (H.name(), ".tif") ||
Path::has_suffix (H.name(), ".TIFF") ||
Path::has_suffix (H.name(), ".TIF")))
Path::has_suffix (H.name(), ".TIF")))
return std::unique_ptr<ImageIO::Base>();

File::TIFF tif (H.name());

uint32 width(0), height(0);
uint16 bpp(0), sampleformat(0), samplesperpixel(0), config (0);
uint32_t width(0), height(0);
uint16_t bpp(0), sampleformat(0), samplesperpixel(0), config (0);
size_t ndir = 0;

do {
Expand All @@ -57,7 +57,7 @@ namespace MR

H.ndim() = samplesperpixel > 1 ? 4 : 3;

H.size(0) = width;
H.size(0) = width;
H.stride(0) = 2;

H.size(1) = height;
Expand All @@ -73,7 +73,7 @@ namespace MR

H.datatype() = DataType::Undefined;
switch (bpp) {
case 8:
case 8:
switch (sampleformat) {
case 1: H.datatype() = DataType::UInt8; break;
case 2: H.datatype() = DataType::Int8; break;
Expand Down Expand Up @@ -114,7 +114,7 @@ namespace MR
if (Path::has_suffix (H.name(), ".tiff") ||
Path::has_suffix (H.name(), ".tif") ||
Path::has_suffix (H.name(), ".TIFF") ||
Path::has_suffix (H.name(), ".TIF"))
Path::has_suffix (H.name(), ".TIF"))
throw Exception ("TIFF format not supported for output");

return false;
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2 changes: 1 addition & 1 deletion core/image_io/tiff.cpp
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Expand Up @@ -36,7 +36,7 @@ namespace MR
for (auto& entry : files) {
File::TIFF tif (entry.name);

uint16 config (0);
uint16_t config (0);
tif.read_and_check (TIFFTAG_PLANARCONFIG, config);

size_t scanline_size = tif.scanline_size();
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