From 4d7a4fc50145e74d0f77eb071076b21467465b4d Mon Sep 17 00:00:00 2001
From: John Hill <john.r.hill@stfc.ac.uk>
Date: Wed, 22 Oct 2014 17:17:54 +0100
Subject: [PATCH] Refs #10397 making changes to handle rotation file
---
.../inc/MantidDataHandling/LoadFITS.h | 4 +-
.../Framework/DataHandling/src/Load.cpp | 6 +-
.../Framework/DataHandling/src/LoadFITS.cpp | 820 ++++++++++--------
.../Framework/DataHandling/src/SaveNXTomo.cpp | 35 +-
4 files changed, 486 insertions(+), 379 deletions(-)
diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadFITS.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadFITS.h
index 1ed0521b906..dcfc964b646 100644
--- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadFITS.h
+++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadFITS.h
@@ -102,7 +102,9 @@ namespace DataHandling
void loadChunkOfBinsFromFile(Mantid::API::MatrixWorkspace_sptr &workspace, vector<vector<double> > &yVals, vector<vector<double> > &eVals, void *&bufferAny, MantidVecPtr &x, size_t spetraCount, int bitsPerPixel, size_t binChunkStartIndex);
/// Initialises a workspace with IDF and fills it with data
API::MatrixWorkspace_sptr initAndPopulateHistogramWorkspace();
-
+ /// Creates a comma separated string of rotations from a file
+ std::string ReadRotations(std::string rotFilePath, size_t fileCount);
+
vector<FITSInfo> m_allHeaderInfo;
size_t m_binChunkSize;
static const int FIXED_HEADER_SIZE = 2880;
diff --git a/Code/Mantid/Framework/DataHandling/src/Load.cpp b/Code/Mantid/Framework/DataHandling/src/Load.cpp
index 0ee51f8d0b4..9bb5bf5f648 100644
--- a/Code/Mantid/Framework/DataHandling/src/Load.cpp
+++ b/Code/Mantid/Framework/DataHandling/src/Load.cpp
@@ -181,10 +181,11 @@ namespace Mantid
// If it's loading into a single file, perform a cursory check on file extensions only.
if((ifl && ifl->loadMutipleAsOne()) || (iflNexus && iflNexus->loadMutipleAsOne()))
{
- if( fileNames[i].substr(fileNames[i].find_last_of(".")) != ext)
+ // Currently disabled for ticket http://trac.mantidproject.org/mantid/ticket/10397 : should be put back in when completing 10231
+ /* if( fileNames[i].substr(fileNames[i].find_last_of(".")) != ext)
{
throw std::runtime_error("Cannot load multiple files when more than one Loader is needed.");
- }
+ }*/
}
else
{
@@ -320,6 +321,7 @@ namespace Mantid
exts.push_back(".h5");
exts.push_back(".hd5");
exts.push_back(".sqw");
+ exts.push_back(".fits");
declareProperty(new MultipleFileProperty("Filename", exts),
"The name of the file(s) to read, including the full or relative "
diff --git a/Code/Mantid/Framework/DataHandling/src/LoadFITS.cpp b/Code/Mantid/Framework/DataHandling/src/LoadFITS.cpp
index 5b200bba28a..904cc0eb089 100644
--- a/Code/Mantid/Framework/DataHandling/src/LoadFITS.cpp
+++ b/Code/Mantid/Framework/DataHandling/src/LoadFITS.cpp
@@ -5,6 +5,7 @@
#include "MantidKernel/UnitFactory.h"
#include <boost/algorithm/string.hpp>
#include <Poco/BinaryReader.h>
+#include <fstream>
using namespace Mantid::DataHandling;
using namespace Mantid::API;
@@ -13,380 +14,463 @@ using namespace std;
using namespace boost;
using Poco::BinaryReader;
+namespace
+{
+ /**
+ * Used with find_if to check a string isn't a fits file (by checking extension)
+ * @param s string to check for extension
+ * @returns bool Value indicating if the string ends with .fits or not
+ */
+ bool IsNotFits(std::string s)
+ {
+ std::string tmp = s;
+ to_lower(tmp);
+ return !ends_with(tmp,".fits");
+ }
+}
namespace Mantid
{
namespace DataHandling
{
- // Register the algorithm into the AlgorithmFactory
- DECLARE_FILELOADER_ALGORITHM(LoadFITS);
-
- /**
- * Return the confidence with with this algorithm can load the file
- * @param descriptor A descriptor for the file
- * @returns An integer specifying the confidence level. 0 indicates it will not be used
- */
- int LoadFITS::confidence(Kernel::FileDescriptor & descriptor) const
- {
- // Should really improve this to check the file header (of first file at least) to make sure it contains the fields wanted
- return (descriptor.extension() == ".fits" || descriptor.extension() == ".fit") ? 80 : 0;
- }
-
- /**
- * Initialise the algorithm. Declare properties which can be set before execution (input) or
- * read from after the execution (output).
- */
- void LoadFITS::init()
- {
- // Specify file extensions which can be associated with a FITS file.
- std::vector<std::string> exts;
-
- // Declare the Filename algorithm property. Mandatory. Sets the path to the file to load.
- exts.clear();
- exts.push_back(".fits");
- exts.push_back(".fit");
-
- declareProperty(new MultipleFileProperty("Filename", exts), "The input filename of the stored data");
- declareProperty(new PropertyWithValue<size_t>("FileChunkSize", 100, Direction::Input), "Number of files to read into memory at a time - use lower values for machines with low memory");
-
- declareProperty(new API::WorkspaceProperty<API::MatrixWorkspace>("OutputWorkspace", "", Kernel::Direction::Output));
- }
-
- /**
- * Execute the algorithm.
- */
- void LoadFITS::exec()
- {
- // Create FITS file information for each file selected
- std::vector<std::string> paths;
- string fName = getPropertyValue("Filename");
- boost::split(paths, fName, boost::is_any_of(","));
- m_binChunkSize = getProperty("FileChunkSize");
-
- // Shrink chunk size to match number of files if it's over the amount (less memory allocated later)
- if(m_binChunkSize > paths.size()) m_binChunkSize = static_cast<int>(paths.size());
-
- m_allHeaderInfo.resize(paths.size());
-
- // Check each header is valid for this loader, - standard (no extension to FITS), and has two axis
- bool headerValid = true;
-
- for(size_t i=0; i<paths.size();++i)
- {
- m_allHeaderInfo[i].extension = "";
- m_allHeaderInfo[i].filePath = paths[i];
- // Get various pieces of information from the file header which are used to create the workspace
- if(parseHeader(m_allHeaderInfo[i]))
- {
- // Get and convert specific standard header values which will help when parsing the data
- // BITPIX, NAXIS, NAXISi (where i = 1..NAXIS, e.g. NAXIS2 for two axis), TOF, TIMEBIN, N_COUNTS, N_TRIGS
- try
- {
- m_allHeaderInfo[i].bitsPerPixel = lexical_cast<int>(m_allHeaderInfo[i].headerKeys["BITPIX"]);
- m_allHeaderInfo[i].numberOfAxis = lexical_cast<int>(m_allHeaderInfo[i].headerKeys["NAXIS"]);
-
- for(int j=0; j<m_allHeaderInfo[i].numberOfAxis; ++j)
- {
- string keyName = "NAXIS" + lexical_cast<string>(j+1);
- m_allHeaderInfo[i].axisPixelLengths.push_back(lexical_cast<int>(m_allHeaderInfo[i].headerKeys[keyName]));
- }
-
- m_allHeaderInfo[i].tof = lexical_cast<double>(m_allHeaderInfo[i].headerKeys["TOF"]);
- m_allHeaderInfo[i].timeBin = lexical_cast<double>(m_allHeaderInfo[i].headerKeys["TIMEBIN"]);
- m_allHeaderInfo[i].countsInImage = lexical_cast<long int>(m_allHeaderInfo[i].headerKeys["N_COUNTS"]);
- m_allHeaderInfo[i].numberOfTriggers = lexical_cast<long int>(m_allHeaderInfo[i].headerKeys["N_TRIGS"]);
- m_allHeaderInfo[i].extension = m_allHeaderInfo[i].headerKeys["XTENSION"]; // Various extensions are available to the FITS format, and must be parsed differently if this is present. Loader doesn't support this.
-
- }
- catch(std::exception &)
- {
- //todo write error and fail this load with invalid data in file.
- g_log.error("Unable to locate one or more valid BITPIX, NAXIS, TOF, TIMEBIN, N_COUNTS or N_TRIGS values in the FITS file header.");
- throw std::runtime_error("Unable to locate one or more valid BITPIX, NAXIS, TOF, TIMEBIN, N_COUNTS or N_TRIGS values in the FITS file header.");
- }
-
- if(m_allHeaderInfo[i].extension != "") headerValid = false;
- if(m_allHeaderInfo[i].numberOfAxis != 2) headerValid = false;
-
- // Test current item has same axis values as first item.
- if(m_allHeaderInfo[0].axisPixelLengths[0] != m_allHeaderInfo[i].axisPixelLengths[0]) headerValid = false;
- if(m_allHeaderInfo[0].axisPixelLengths[1] != m_allHeaderInfo[i].axisPixelLengths[1]) headerValid = false;
- }
- else
- {
- // Unable to parse the header, throw.
- g_log.error("Unable to open the FITS file.");
- throw std::runtime_error("Unable to open the FITS file.");
- }
-
- }
-
- // Check that the files use bit depths of either 8, 16 or 32
- if(m_allHeaderInfo[0].bitsPerPixel != 8 && m_allHeaderInfo[0].bitsPerPixel != 16 && m_allHeaderInfo[0].bitsPerPixel != 32)
- {
- g_log.error("FITS Loader only supports 8, 16 or 32 bits per pixel.");
- throw std::runtime_error("FITS loader only supports 8, 16 or 32 bits per pixel.");
- }
-
- // Check the format is correct and create the Workspace
- if(headerValid)
- {
- // No extension is set, therefore it's the standard format which we can parse.
-
- // Delete the output workspace name if it existed
- std::string outName = getPropertyValue("OutputWorkspace");
- if (AnalysisDataService::Instance().doesExist(outName)) AnalysisDataService::Instance().remove(outName);
-
- MatrixWorkspace_sptr ws;
-
- ws = initAndPopulateHistogramWorkspace();
-
- // Assign it to the output workspace property
- setProperty("OutputWorkspace",ws);
- }
- else
- {
- // Invalid files, record error
- g_log.error("Loader currently doesn't support FITS files with non-standard extensions, greater than two axis of data, or has detected that all the files are not similar.");
- throw std::runtime_error("Loader currently doesn't support FITS files with non-standard extensions, greater than two axis of data, or has detected that all the files are not similar.");
- }
- }
-
- /**
- * Read a single files header and populate an object with the information
- * @param headerInfo A FITSInfo file object to parse header information into
- * @returns A bool specifying succes of the operation
- */
- bool LoadFITS::parseHeader(FITSInfo &headerInfo)
- {
- bool ranSuccessfully = true;
- try
- {
- ifstream istr(headerInfo.filePath.c_str(), ios::binary);
- Poco::BinaryReader reader(istr);
-
- // Iterate 80 bytes at a time until header is parsed | 2880 bytes is the fixed header length of FITS
- // 2880/80 = 36 iterations required
- for(int i=0; i < 36; ++i)
- {
- // Keep vect of each header item, including comments, and also keep a map of individual keys.
- string part;
- reader.readRaw(80,part);
- headerInfo.headerItems.push_back(part);
-
- // Add key/values - these are separated by the = symbol.
- // If it doesn't have an = it's a comment to ignore. All keys should be unique
- auto eqPos = part.find('=');
- if(eqPos > 0)
- {
- string key = part.substr(0, eqPos);
- string value = part.substr(eqPos+1);
-
- // Comments are added after the value separated by a / symbol. Remove.
- auto slashPos = value.find('/');
- if(slashPos > 0) value = value.substr(0, slashPos);
+ // Register the algorithm into the AlgorithmFactory
+ DECLARE_FILELOADER_ALGORITHM(LoadFITS);
+
+ /**
+ * Return the confidence with with this algorithm can load the file
+ * @param descriptor A descriptor for the file
+ * @returns An integer specifying the confidence level. 0 indicates it will not be used
+ */
+ int LoadFITS::confidence(Kernel::FileDescriptor & descriptor) const
+ {
+ // Should really improve this to check the file header (of first file at least) to make sure it contains the fields wanted
+ return (descriptor.extension() == ".fits" || descriptor.extension() == ".fit") ? 80 : 0;
+ }
+
+ /**
+ * Initialise the algorithm. Declare properties which can be set before execution (input) or
+ * read from after the execution (output).
+ */
+ void LoadFITS::init()
+ {
+ // Specify file extensions which can be associated with a FITS file.
+ std::vector<std::string> exts;
+
+ // Declare the Filename algorithm property. Mandatory. Sets the path to the file to load.
+ exts.clear();
+ exts.push_back(".fits");
+ exts.push_back(".fit");
+
+ declareProperty(new MultipleFileProperty("Filename", exts), "The input filename of the stored data");
+ declareProperty(new PropertyWithValue<size_t>("FileChunkSize", 100, Direction::Input), "Number of files to read into memory at a time - use lower values for machines with low memory");
+
+ declareProperty(new API::WorkspaceProperty<API::MatrixWorkspace>("OutputWorkspace", "", Kernel::Direction::Output));
+ }
+
+ /**
+ * Execute the algorithm.
+ */
+ void LoadFITS::exec()
+ {
+ // Create FITS file information for each file selected
+ std::vector<std::string> paths;
+ string fName = getPropertyValue("Filename");
+ boost::split(paths, fName, boost::is_any_of(","));
+ m_binChunkSize = getProperty("FileChunkSize");
+
+ // If paths contains a non fits file, assume (for now) that it contains information about the rotations
+ std::string rotFilePath = "";
+ std::vector<std::string>::iterator it = std::find_if(paths.begin(),paths.end(),IsNotFits);
+ if(it != paths.end())
+ {
+ rotFilePath = *it;
+ paths.erase(it);
+ }
+
+ // Shrink chunk size to match number of files if it's over the amount (less memory allocated later)
+ if(m_binChunkSize > paths.size()) m_binChunkSize = static_cast<int>(paths.size());
+
+ m_allHeaderInfo.resize(paths.size());
+
+ // Check each header is valid for this loader, - standard (no extension to FITS), and has two axis
+ bool headerValid = true;
+
+ for(size_t i=0; i<paths.size();++i)
+ {
+ m_allHeaderInfo[i].extension = "";
+ m_allHeaderInfo[i].filePath = paths[i];
+ // Get various pieces of information from the file header which are used to create the workspace
+ if(parseHeader(m_allHeaderInfo[i]))
+ {
+ // Get and convert specific standard header values which will help when parsing the data
+ // BITPIX, NAXIS, NAXISi (where i = 1..NAXIS, e.g. NAXIS2 for two axis), TOF, TIMEBIN, N_COUNTS, N_TRIGS
+ try
+ {
+ string tmpBitPix = m_allHeaderInfo[i].headerKeys["BITPIX"];
+ if(boost::contains(tmpBitPix, "-"))
+ boost::erase_all(tmpBitPix,"-");
+ m_allHeaderInfo[i].bitsPerPixel = lexical_cast<int>(tmpBitPix);
+ m_allHeaderInfo[i].numberOfAxis = lexical_cast<int>(m_allHeaderInfo[i].headerKeys["NAXIS"]);
+
+ for(int j=0; j<m_allHeaderInfo[i].numberOfAxis; ++j)
+ {
+ string keyName = "NAXIS" + lexical_cast<string>(j+1);
+ m_allHeaderInfo[i].axisPixelLengths.push_back(lexical_cast<int>(m_allHeaderInfo[i].headerKeys[keyName]));
+ }
+
+ //m_allHeaderInfo[i].tof = lexical_cast<double>(m_allHeaderInfo[i].headerKeys["TOF"]);
+ //m_allHeaderInfo[i].timeBin = lexical_cast<double>(m_allHeaderInfo[i].headerKeys["TIMEBIN"]);
+ //m_allHeaderInfo[i].countsInImage = lexical_cast<long int>(m_allHeaderInfo[i].headerKeys["N_COUNTS"]);
+ //m_allHeaderInfo[i].numberOfTriggers = lexical_cast<long int>(m_allHeaderInfo[i].headerKeys["N_TRIGS"]);
+ m_allHeaderInfo[i].extension = m_allHeaderInfo[i].headerKeys["XTENSION"]; // Various extensions are available to the FITS format, and must be parsed differently if this is present. Loader doesn't support this.
+
+ }
+ catch(std::exception &)
+ {
+ //todo write error and fail this load with invalid data in file.
+ throw std::runtime_error("Unable to locate one or more valid BITPIX, NAXIS, TOF, TIMEBIN, N_COUNTS or N_TRIGS values in the FITS file header.");
+ }
+
+ if(m_allHeaderInfo[i].extension != "") headerValid = false;
+ if(m_allHeaderInfo[i].numberOfAxis != 2) headerValid = false;
+
+ // Test current item has same axis values as first item.
+ if(m_allHeaderInfo[0].axisPixelLengths[0] != m_allHeaderInfo[i].axisPixelLengths[0]) headerValid = false;
+ if(m_allHeaderInfo[0].axisPixelLengths[1] != m_allHeaderInfo[i].axisPixelLengths[1]) headerValid = false;
+ }
+ else
+ {
+ // Unable to parse the header, throw.
+ throw std::runtime_error("Unable to open the FITS file.");
+ }
+
+ }
+
+ // Check that the files use bit depths of either 8, 16 or 32
+ if(m_allHeaderInfo[0].bitsPerPixel != 8 && m_allHeaderInfo[0].bitsPerPixel != 16 && m_allHeaderInfo[0].bitsPerPixel != 32)
+ {
+ throw std::runtime_error("FITS loader only supports 8, 16 or 32 bits per pixel.");
+ }
+
+ // Check the format is correct and create the Workspace
+ if(headerValid)
+ {
+ // No extension is set, therefore it's the standard format which we can parse.
+
+ // Delete the output workspace name if it existed
+ std::string outName = getPropertyValue("OutputWorkspace");
+ if (AnalysisDataService::Instance().doesExist(outName)) AnalysisDataService::Instance().remove(outName);
+
+ MatrixWorkspace_sptr ws;
+
+ ws = initAndPopulateHistogramWorkspace();
+
+ // Set info in WS log to hold rotational information
+ if(rotFilePath != "")
+ {
+ string csvRotations = ReadRotations(rotFilePath, paths.size());
+ Run &theRun = ws->mutableRun();
+ theRun.addLogData(new PropertyWithValue<std::string>("Rotations", csvRotations));
+ }
+
+ // Assign it to the output workspace property
+ setProperty("OutputWorkspace",ws);
+ }
+ else
+ {
+ // Invalid files, record error
+ throw std::runtime_error("Loader currently doesn't support FITS files with non-standard extensions, greater than two axis of data, or has detected that all the files are not similar.");
+ }
+ }
+
+ /**
+ * Read a single files header and populate an object with the information
+ * @param headerInfo A FITSInfo file object to parse header information into
+ * @returns A bool specifying succes of the operation
+ */
+ bool LoadFITS::parseHeader(FITSInfo &headerInfo)
+ {
+ bool ranSuccessfully = true;
+ try
+ {
+ ifstream istr(headerInfo.filePath.c_str(), ios::binary);
+ Poco::BinaryReader reader(istr);
+
+ // Iterate 80 bytes at a time until header is parsed | 2880 bytes is the fixed header length of FITS
+ // 2880/80 = 36 iterations required
+ for(int i=0; i < 36; ++i)
+ {
+ // Keep vect of each header item, including comments, and also keep a map of individual keys.
+ string part;
+ reader.readRaw(80,part);
+ headerInfo.headerItems.push_back(part);
+
+ // Add key/values - these are separated by the = symbol.
+ // If it doesn't have an = it's a comment to ignore. All keys should be unique
+ auto eqPos = part.find('=');
+ if(eqPos > 0)
+ {
+ string key = part.substr(0, eqPos);
+ string value = part.substr(eqPos+1);
+
+ // Comments are added after the value separated by a / symbol. Remove.
+ auto slashPos = value.find('/');
+ if(slashPos > 0) value = value.substr(0, slashPos);
- boost::trim(key);
- boost::trim(value);
- headerInfo.headerKeys[key] = value;
- }
- }
-
- istr.close();
- }
- catch(...)
- {
- // Unable to read the file
- ranSuccessfully = false;
- }
-
- return ranSuccessfully;
- }
-
- /**
- * Create histogram workspace
- * @returns Created workspace
- */
- MatrixWorkspace_sptr LoadFITS::initAndPopulateHistogramWorkspace()
- {
- MantidVecPtr x;
- x.access().resize(m_allHeaderInfo.size() + 1);
-
- // Init time bins
- double binCount = 0;
- for(size_t i=0;i<m_allHeaderInfo.size() + 1; ++i)
- {
- x.access()[i] = binCount;
- if(i != m_allHeaderInfo.size()) binCount += m_allHeaderInfo[i].timeBin;
- }
-
- size_t spectraCount = 0;
- if(m_allHeaderInfo[0].numberOfAxis > 0) spectraCount += m_allHeaderInfo[0].axisPixelLengths[0];
-
- // Presumably 2 axis, but futureproofing.
- for(int i=1;i<m_allHeaderInfo[0].numberOfAxis;++i)
- {
- spectraCount *= m_allHeaderInfo[0].axisPixelLengths[i];
- }
-
- MatrixWorkspace_sptr retVal(new DataObjects::Workspace2D);
- retVal->initialize(spectraCount, m_allHeaderInfo.size()+1, m_allHeaderInfo.size());
-
- IAlgorithm_sptr loadInst = createChildAlgorithm("LoadInstrument");
+ boost::trim(key);
+ boost::trim(value);
+ headerInfo.headerKeys[key] = value;
+ }
+ }
+
+ istr.close();
+ }
+ catch(...)
+ {
+ // Unable to read the file
+ ranSuccessfully = false;
+ }
+
+ return ranSuccessfully;
+ }
+
+ /**
+ * Create histogram workspace
+ * @returns Created workspace
+ */
+ MatrixWorkspace_sptr LoadFITS::initAndPopulateHistogramWorkspace()
+ {
+ MantidVecPtr x;
+ x.access().resize(m_allHeaderInfo.size() + 1);
+
+ // Init time bins
+ double binCount = 0;
+ for(size_t i=0;i<m_allHeaderInfo.size() + 1; ++i)
+ {
+ x.access()[i] = binCount;
+ if(i != m_allHeaderInfo.size()) binCount += 1;//m_allHeaderInfo[i].timeBin;
+ }
+
+ size_t spectraCount = 0;
+ if(m_allHeaderInfo[0].numberOfAxis > 0) spectraCount += m_allHeaderInfo[0].axisPixelLengths[0];
+
+ // Presumably 2 axis, but futureproofing.
+ for(int i=1;i<m_allHeaderInfo[0].numberOfAxis;++i)
+ {
+ spectraCount *= m_allHeaderInfo[0].axisPixelLengths[i];
+ }
+
+ MatrixWorkspace_sptr retVal(new DataObjects::Workspace2D);
+ retVal->initialize(spectraCount, m_allHeaderInfo.size()+1, m_allHeaderInfo.size());
+
+ IAlgorithm_sptr loadInst = createChildAlgorithm("LoadInstrument");
- try
- {
- std::string directoryName = Kernel::ConfigService::Instance().getInstrumentDirectory();
- directoryName = directoryName + "/IMAT_Definition.xml";
-
- loadInst->setPropertyValue("Filename", directoryName);
- loadInst->setProperty<MatrixWorkspace_sptr>("Workspace", retVal);
- loadInst->execute();
- }
- catch (std::exception & ex)
- {
- g_log.information("Cannot load the instrument definition. " + string(ex.what()) );
- }
-
- int bitsPerPixel = m_allHeaderInfo[0].bitsPerPixel; // assumes all files have the same, which they should.
- vector<vector<double> > yVals(spectraCount, std::vector<double>(m_binChunkSize));
- vector<vector<double> > eVals(spectraCount, std::vector<double>(m_binChunkSize));
-
- // allocate memory to contain the data section of the file:
- void * bufferAny = NULL;
- bufferAny = malloc ((bitsPerPixel/8)*spectraCount);
-
- if (bufferAny == NULL)
- {
- throw std::runtime_error("FITS loader couldn't allocate enough memory to run. Try a smaller chunk size.");
- }
-
- size_t steps = static_cast<size_t>(ceil(m_allHeaderInfo.size()/m_binChunkSize));
- Progress prog(this,0.0,1.0,steps);
-
- // Load a chunk of files at a time into workspace
- try
- {
- for(size_t i=0; i<m_allHeaderInfo.size(); i+=m_binChunkSize)
- {
- loadChunkOfBinsFromFile(retVal, yVals, eVals, bufferAny, x, spectraCount, bitsPerPixel, i);
- prog.report(name());
- }
- }
- catch(...)
- {
- // Exceptions should be handled internally, but catch here to free any memory. Belt and braces.
- free(bufferAny);
- g_log.error("FITS Loader unable to correctly parse files.");
- throw std::runtime_error("FITS loader unable to correctly parse files.");
- }
-
- // Memory no longer needed
- free (bufferAny);
-
- retVal->mutableRun().addProperty("Filename", m_allHeaderInfo[0].filePath);
-
- // Set the Unit of the X Axis
- try
- {
- retVal->getAxis(0)->unit() = UnitFactory::Instance().create("TOF");
- }
- catch ( Exception::NotFoundError & )
- {
- retVal->getAxis(0)->unit() = UnitFactory::Instance().create("Label");
- Unit_sptr unit = retVal->getAxis(0)->unit();
- boost::shared_ptr<Units::Label> label = boost::dynamic_pointer_cast<Units::Label>(unit);
- label->setLabel("TOF", "TOF");
- }
-
- retVal->setYUnit("Counts");
- retVal->setTitle("Test Workspace");
-
- return retVal;
- }
-
- /**
- * Loads data from a selection of the FITS files into the workspace
- * @param workspace The workspace to insert data into
- * @param yVals Reference to a pre-allocated vector to hold data values for the workspace
- * @param eVals Reference to a pre-allocated vector to hold error values for the workspace
- * @param bufferAny Pointer to an allocated memory region which will hold a files worth of data
- * @param x Vector holding the X bin values
- * @param spectraCount Number of data points in each file
- * @param bitsPerPixel Number of bits used to represent one data point
- * @param binChunkStartIndex Index for the first file to be processed in this chunk
- */
- void LoadFITS::loadChunkOfBinsFromFile(MatrixWorkspace_sptr &workspace, vector<vector<double> > &yVals, vector<vector<double> > &eVals, void *&bufferAny, MantidVecPtr &x, size_t spectraCount, int bitsPerPixel, size_t binChunkStartIndex)
- {
- size_t binsThisChunk = m_binChunkSize;
- if((binChunkStartIndex + m_binChunkSize) > m_allHeaderInfo.size())
- {
- // No need to do extra processing if number of bins to process is lower than m_binChunkSize
- // Also used to prevent out of bounds error where a greater number of elements have been reserved.
- binsThisChunk = static_cast<size_t>(m_allHeaderInfo.size() - binChunkStartIndex);
- }
-
- uint8_t *buffer8 = NULL;
- uint16_t *buffer16 = NULL;
- uint32_t *buffer32 = NULL;
-
- // create pointer of correct data type to void pointer of the buffer:
- buffer8 = static_cast<uint8_t*>(bufferAny);
- buffer16 = static_cast<uint16_t*>(bufferAny);
- buffer32 = static_cast<uint32_t*>(bufferAny);
-
- for(size_t i=binChunkStartIndex; i < binChunkStartIndex+binsThisChunk ; ++i)
- {
- // Read Data
- bool fileErr = false;
- FILE * currFile = fopen ( m_allHeaderInfo[i].filePath.c_str(), "rb" );
- if (currFile==NULL) fileErr = true;
-
- size_t result = 0;
- if(!fileErr)
- {
- fseek (currFile , FIXED_HEADER_SIZE , SEEK_CUR);
- result = fread(bufferAny, bitsPerPixel/8, spectraCount, currFile);
- }
-
- if (result != spectraCount) fileErr = true;
-
- if(fileErr)
- {
- throw std::runtime_error("Error reading file; possibly invalid data.");
- }
-
- for(size_t j=0; j<spectraCount;++j)
- {
- double val = 0;
- if(bitsPerPixel == 8) val = static_cast<double>(buffer8[j]);
- if(bitsPerPixel == 16) val = static_cast<double>(buffer16[j]);
- if(bitsPerPixel == 32) val = static_cast<double>(buffer32[j]);
-
- yVals[j][i-binChunkStartIndex] = val;
- eVals[j][i-binChunkStartIndex] = sqrt(val);
- }
-
- // Clear memory associated with the file load
- fclose (currFile);
- }
-
- // Now load chunk into workspace
- PARALLEL_FOR1(workspace)
- for (int64_t wi = 0; wi < static_cast<int64_t>(spectraCount); ++wi)
- {
- workspace->setX(wi, x);
- MantidVec *currY = &workspace->dataY(wi);
- MantidVec *currE = &workspace->dataE(wi);
-
- std::copy(yVals[wi].begin(), yVals[wi].end()-(m_binChunkSize-binsThisChunk), currY->begin()+binChunkStartIndex );
- std::copy(eVals[wi].begin(), eVals[wi].end()-(m_binChunkSize-binsThisChunk), currE->begin()+binChunkStartIndex );
-
- // I expect this will be wanted once IDF is in a more useful state.
- //workspace->getSpectrum(wi)->setDetectorID(detid_t(wi));
- //workspace->getSpectrum(wi)->setSpectrumNo(specid_t(wi+1));
- }
- }
+ try
+ {
+ std::string directoryName = Kernel::ConfigService::Instance().getInstrumentDirectory();
+ directoryName = directoryName + "/IMAT_Definition.xml";
+
+ loadInst->setPropertyValue("Filename", directoryName);
+ loadInst->setProperty<MatrixWorkspace_sptr>("Workspace", retVal);
+ loadInst->execute();
+ }
+ catch (std::exception & ex)
+ {
+ g_log.information("Cannot load the instrument definition. " + string(ex.what()) );
+ }
+
+ int bitsPerPixel = m_allHeaderInfo[0].bitsPerPixel; // assumes all files have the same, which they should.
+ vector<vector<double> > yVals(spectraCount, std::vector<double>(m_binChunkSize));
+ vector<vector<double> > eVals(spectraCount, std::vector<double>(m_binChunkSize));
+
+ // allocate memory to contain the data section of the file:
+ void * bufferAny = NULL;
+ bufferAny = malloc ((bitsPerPixel/8)*spectraCount);
+
+ if (bufferAny == NULL)
+ {
+ throw std::runtime_error("FITS loader couldn't allocate enough memory to run. Try a smaller chunk size.");
+ }
+
+ size_t steps = static_cast<size_t>(ceil(m_allHeaderInfo.size()/m_binChunkSize));
+ Progress prog(this,0.0,1.0,steps);
+
+ // Load a chunk of files at a time into workspace
+ try
+ {
+ for(size_t i=0; i<m_allHeaderInfo.size(); i+=m_binChunkSize)
+ {
+ loadChunkOfBinsFromFile(retVal, yVals, eVals, bufferAny, x, spectraCount, bitsPerPixel, i);
+ prog.report(name());
+ }
+ }
+ catch(...)
+ {
+ // Exceptions should be handled internally, but catch here to free any memory. Belt and braces.
+ free(bufferAny);
+ throw std::runtime_error("FITS loader unable to correctly parse files.");
+ }
+
+ // Memory no longer needed
+ free (bufferAny);
+
+ retVal->mutableRun().addProperty("Filename", m_allHeaderInfo[0].filePath);
+
+ // Set the Unit of the X Axis
+ try
+ {
+ retVal->getAxis(0)->unit() = UnitFactory::Instance().create("TOF");
+ }
+ catch ( Exception::NotFoundError & )
+ {
+ retVal->getAxis(0)->unit() = UnitFactory::Instance().create("Label");
+ Unit_sptr unit = retVal->getAxis(0)->unit();
+ boost::shared_ptr<Units::Label> label = boost::dynamic_pointer_cast<Units::Label>(unit);
+ label->setLabel("TOF", "TOF");
+ }
+
+ retVal->setYUnit("Counts");
+ retVal->setTitle("Test Workspace");
+
+ return retVal;
+ }
+
+ /**
+ * Loads data from a selection of the FITS files into the workspace
+ * @param workspace The workspace to insert data into
+ * @param yVals Reference to a pre-allocated vector to hold data values for the workspace
+ * @param eVals Reference to a pre-allocated vector to hold error values for the workspace
+ * @param bufferAny Pointer to an allocated memory region which will hold a files worth of data
+ * @param x Vector holding the X bin values
+ * @param spectraCount Number of data points in each file
+ * @param bitsPerPixel Number of bits used to represent one data point
+ * @param binChunkStartIndex Index for the first file to be processed in this chunk
+ */
+ void LoadFITS::loadChunkOfBinsFromFile(MatrixWorkspace_sptr &workspace, vector<vector<double> > &yVals, vector<vector<double> > &eVals, void *&bufferAny, MantidVecPtr &x, size_t spectraCount, int bitsPerPixel, size_t binChunkStartIndex)
+ {
+ size_t binsThisChunk = m_binChunkSize;
+ if((binChunkStartIndex + m_binChunkSize) > m_allHeaderInfo.size())
+ {
+ // No need to do extra processing if number of bins to process is lower than m_binChunkSize
+ // Also used to prevent out of bounds error where a greater number of elements have been reserved.
+ binsThisChunk = static_cast<size_t>(m_allHeaderInfo.size() - binChunkStartIndex);
+ }
+
+ uint8_t *buffer8 = NULL;
+ uint16_t *buffer16 = NULL;
+ uint32_t *buffer32 = NULL;
+
+ // create pointer of correct data type to void pointer of the buffer:
+ buffer8 = static_cast<uint8_t*>(bufferAny);
+ buffer16 = static_cast<uint16_t*>(bufferAny);
+ buffer32 = static_cast<uint32_t*>(bufferAny);
+
+ for(size_t i=binChunkStartIndex; i < binChunkStartIndex+binsThisChunk ; ++i)
+ {
+ // Read Data
+ bool fileErr = false;
+ FILE * currFile = fopen ( m_allHeaderInfo[i].filePath.c_str(), "rb" );
+ if (currFile==NULL) fileErr = true;
+
+ size_t result = 0;
+ if(!fileErr)
+ {
+ fseek (currFile , FIXED_HEADER_SIZE , SEEK_CUR);
+ result = fread(bufferAny, bitsPerPixel/8, spectraCount, currFile);
+ }
+
+ if (result != spectraCount) fileErr = true;
+
+ if(fileErr)
+ {
+ throw std::runtime_error("Error reading file; possibly invalid data.");
+ }
+
+ for(size_t j=0; j<spectraCount;++j)
+ {
+ double val = 0;
+ if(bitsPerPixel == 8) val = static_cast<double>(buffer8[j]);
+ if(bitsPerPixel == 16) val = static_cast<double>(buffer16[j]);
+ if(bitsPerPixel == 32) val = static_cast<double>(buffer32[j]);
+
+ yVals[j][i-binChunkStartIndex] = val;
+ eVals[j][i-binChunkStartIndex] = sqrt(val);
+ }
+
+ // Clear memory associated with the file load
+ fclose (currFile);
+ }
+
+ // Now load chunk into workspace
+ PARALLEL_FOR1(workspace)
+ for (int64_t wi = 0; wi < static_cast<int64_t>(spectraCount); ++wi)
+ {
+ workspace->setX(wi, x);
+ MantidVec *currY = &workspace->dataY(wi);
+ MantidVec *currE = &workspace->dataE(wi);
+
+ std::copy(yVals[wi].begin(), yVals[wi].end()-(m_binChunkSize-binsThisChunk), currY->begin()+binChunkStartIndex );
+ std::copy(eVals[wi].begin(), eVals[wi].end()-(m_binChunkSize-binsThisChunk), currE->begin()+binChunkStartIndex );
+
+ // I expect this will be wanted once IDF is in a more useful state.
+ //workspace->getSpectrum(wi)->setDetectorID(detid_t(wi));
+ //workspace->getSpectrum(wi)->setSpectrumNo(specid_t(wi+1));
+ }
+ }
+
+ /**
+ * Reads a file containing rotation values for each image into a comma separated string
+ * @param rotFilePath The path to a file containing rotation values
+ * @param fileCount number of images which should have corresponding rotation values in the file
+ *
+ * @returns string A comma separated string of doubles
+ */
+ std::string LoadFITS::ReadRotations(std::string rotFilePath, size_t fileCount)
+ {
+ ifstream fStream(rotFilePath);
+ std::string csvRotations = "";
+
+ try
+ {
+ // Ensure valid file
+ if(fStream.good())
+ {
+ // Get lines, split words, verify and add to map.
+ string line;
+ vector<string> lineSplit;
+ size_t ind = -1;
+ while(getline(fStream, line))
+ {
+ ind++;
+ boost::split(lineSplit,line, boost::is_any_of("\t"));
+
+ if(ind==0 || lineSplit[0] == "")
+ continue; // Skip first iteration or where rotation value is empty
+
+ if(ind!=1) // append a comma to separate values if not the first index
+ csvRotations += ",";
+
+ csvRotations += lineSplit[1];
+ }
+
+ // Check the number of rotations in file matches number of files
+ if(ind != fileCount)
+ throw std::runtime_error("File error, throw higher up.");
+
+ fStream.close();
+ }
+ else
+ {
+ throw std::runtime_error("File error, throw higher up.");
+ }
+ }
+ catch(...)
+ {
+ throw std::runtime_error("Invalid file path or file format: Expected a file with a line separated list of rotations with the same number of entries as other files.");
+ }
+
+ return csvRotations;
+ }
+
}
}
-
diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp
index 836047e6fb0..70b590cd733 100644
--- a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp
+++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp
@@ -152,19 +152,38 @@ namespace Mantid
// TODO: Write sample info
// name
- std::vector<double> rotationAngles(dims_array[0]);
// Initialise rotations - if unknown, fill with equal steps from 0 to 180 over all frames.
- // TODO: collect and use actual rotation values
-
- double step = static_cast<double>(180/dims_array[0]);
- rotationAngles[0] = step;
+ std::vector<double> rotationAngles(dims_array[0]);
+ std::string rotValues = "";
+ std::vector<std::string> rotSplit;
- for(auto it = rotationAngles.begin()+1; it != rotationAngles.end(); ++it)
+ if(inputWS->run().hasProperty("Rotations"))
+ {
+ rotValues = inputWS->run().getLogData("Rotations")->value();
+ boost::split(rotSplit, rotValues, boost::is_any_of(","));
+ }
+
+ if(rotSplit.size() == static_cast<size_t>(dims_array[0]) )
+ {
+ for(size_t i=0; i<rotSplit.size(); i++)
+ {
+ rotationAngles[i] = boost::lexical_cast<double>(rotSplit[i]);
+ }
+ }
+ else
{
- *it = (*(it-1)) + step;
+ // Make some fake values
+ g_log.notice("Unable to find a correctly formatted rotation angle file with same entry count as input; creating fake values.");
+ double step = static_cast<double>(180/dims_array[0]);
+ rotationAngles[0] = step;
+
+ for(auto it = rotationAngles.begin()+1; it != rotationAngles.end(); ++it)
+ {
+ *it = (*(it-1)) + step;
+ }
}
- nxFile.writeData("rotation_angle", rotationAngles);
+ nxFile.writeData("rotation_angle", rotationAngles);
// Create a link object for rotation_angle to use later
nxFile.openData("rotation_angle");
--
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