diff --git a/Framework/DataHandling/inc/MantidDataHandling/LoadFITS.h b/Framework/DataHandling/inc/MantidDataHandling/LoadFITS.h
index 182948f59e25cd6e2da040e13a79c38274d8c9ac..f39253429325c0939686951161d2571880e011cc 100644
--- a/Framework/DataHandling/inc/MantidDataHandling/LoadFITS.h
+++ b/Framework/DataHandling/inc/MantidDataHandling/LoadFITS.h
@@ -97,27 +97,30 @@ private:
/// Execution code
void exec();
- /// Loads files into workspace(s)
- void doLoadFiles(const std::vector<std::string> &paths,
- const std::string &outWSName, bool loadAsRectImg = false);
-
/// Loads the FITS header(s) into a struct
void doLoadHeaders(const std::vector<std::string> &paths,
std::vector<FITSInfo> &headers);
+ /// Once loaded, check against standard and limitations of this algorithm
+ void headerSanityCheck(const FITSInfo &hdr, const FITSInfo &hdrFirst);
+
+ /// Loads files into workspace(s)
+ void doLoadFiles(const std::vector<std::string> &paths,
+ const std::string &outWSName, bool loadAsRectImg,
+ int binSize, double noiseThresh);
+
/// Parses the header values for the FITS file
void parseHeader(FITSInfo &headerInfo);
/// Initialises a workspace with IDF and fills it with data
- DataObjects::Workspace2D_sptr
- makeWorkspace(const FITSInfo &fileInfo, size_t &newFileNumber,
- std::vector<char> &buffer, API::MantidImage &imageY,
- API::MantidImage &imageE,
- const DataObjects::Workspace2D_sptr parent,
- bool loadAsRectImg = false);
+ DataObjects::Workspace2D_sptr makeWorkspace(
+ const FITSInfo &fileInfo, size_t &newFileNumber,
+ std::vector<char> &buffer, API::MantidImage &imageY,
+ API::MantidImage &imageE, const DataObjects::Workspace2D_sptr parent,
+ bool loadAsRectImg = false, int binSize = 1, double noiseThresh = false);
void addAxesInfoAndLogs(DataObjects::Workspace2D_sptr ws, bool loadAsRectImg,
- const FITSInfo &fileInfo, double cmpp);
+ const FITSInfo &fileInfo, int binSize, double cmpp);
// Reads the data from a single FITS file into a workspace (directly, fast)
void readDataToWorkspace(const FITSInfo &fileInfo, double cmpp,
@@ -132,9 +135,6 @@ private:
void readInBuffer(const FITSInfo &fileInfo, std::vector<char> &buffer,
size_t len);
- /// Once loaded, check against standard and limitations of this algorithm
- void headerSanityCheck(const FITSInfo &hdr, const FITSInfo &hdrFirst);
-
/// filter noise pixel by pixel
void doFilterNoise(double thresh, API::MantidImage &imageY,
API::MantidImage &imageE);
@@ -148,16 +148,16 @@ private:
void setupDefaultKeywordNames();
+ // Maps the header keys to specified values
+ void mapHeaderKeys();
+
/// Returns the trailing number from a string minus leading 0's (so 25 from
- /// workspace_00025)
+ /// workspace_000025)
size_t fetchNumber(const std::string &name);
// Adds a number of leading 0's to another number up to the totalDigitCount.
std::string padZeros(const size_t number, const size_t totalDigitCount);
- // Maps the header keys to specified values
- void mapHeaderKeys();
-
// Strings used to map header keys
std::string m_headerScaleKey;
std::string m_headerOffsetKey;
@@ -176,14 +176,10 @@ private:
std::string m_baseName;
size_t m_pixelCount;
- // rebin block size (m_rebin x m_rebin) cells
- int m_rebin;
- // noise threshold level
- double m_noiseThresh;
// Number of digits for the fixed width appendix number added to
// workspace names, i.e. 3=> workspace_001; 5 => workspace_00001
- static const size_t g_DIGIT_SIZE_APPEND = 5;
+ static const size_t g_DIGIT_SIZE_APPEND = 6;
/// size of a FITS header block (room for 36 entries, of 80
/// characters each), in bytes. A FITS header always comes in
/// multiples of this block.
diff --git a/Framework/DataHandling/src/LoadFITS.cpp b/Framework/DataHandling/src/LoadFITS.cpp
index 4c1f2309c9a043dc8a2ca153b4fed530a2942282..1b9e77436175fc5b005c3798f54a2191d6324975 100644
--- a/Framework/DataHandling/src/LoadFITS.cpp
+++ b/Framework/DataHandling/src/LoadFITS.cpp
@@ -37,8 +37,7 @@ const std::string LoadFITS::g_defaultImgType = "SAMPLE";
LoadFITS::LoadFITS()
: m_headerScaleKey(), m_headerOffsetKey(), m_headerBitDepthKey(),
m_headerRotationKey(), m_headerImageKeyKey(), m_headerAxisNameKeys(),
- m_mapFile(), m_baseName(), m_pixelCount(0), m_rebin(1),
- m_noiseThresh(0.0) {
+ m_mapFile(), m_baseName(), m_pixelCount(0) {
setupDefaultKeywordNames();
}
@@ -56,31 +55,6 @@ int LoadFITS::confidence(Kernel::FileDescriptor &descriptor) const {
: 0;
}
-/**
- * Sets several keyword names with default (and standard) values. You
- * don't want to change these unless you want to break compatibility
- * with the FITS standard.
- */
-void LoadFITS::setupDefaultKeywordNames() {
- // Inits all the absolutely necessary keywords
- // standard headers (If SIMPLE=T)
- m_headerScaleKey = "BSCALE";
- m_headerOffsetKey = "BZERO";
- m_headerBitDepthKey = "BITPIX";
- m_headerImageKeyKey = "IMAGE_TYPE"; // This is a "HIERARCH Image/Type= "
- m_headerRotationKey = "ROTATION";
-
- m_headerNAxisNameKey = "NAXIS";
- m_headerAxisNameKeys.push_back("NAXIS1");
- m_headerAxisNameKeys.push_back("NAXIS2");
-
- m_mapFile = "";
-
- // extensions
- m_sampleRotation = "HIERARCH Sample/Tomo_Angle";
- m_imageType = "HIERARCH Image/Type";
-}
-
/**
* Initialise the algorithm. Declare properties which can be set before execution
* (input) or
@@ -147,149 +121,12 @@ void LoadFITS::exec() {
std::vector<std::string> paths;
boost::split(paths, fName, boost::is_any_of(","));
- m_rebin = getProperty("BinSize");
- m_noiseThresh = getProperty("FilterNoiseLevel");
+ int binSize = getProperty("BinSize");
+ double noiseThresh = getProperty("FilterNoiseLevel");
bool loadAsRectImg = getProperty("LoadAsRectImg");
const std::string outWSName = getPropertyValue("OutputWorkspace");
- doLoadFiles(paths, outWSName, loadAsRectImg);
-}
-
-/**
- * Create FITS file information for each file selected. Loads headers
- * and data from the files and creates and fills the output
- * workspace(s).
- *
- * @param paths File names as given in the algorithm input property
- *
- * @param outWSName name of the output (group) workspace to create
- *
- * @param loadAsRectImg Load files with 1 spectrum per row and 1 bin
- * per column, so a color fill plot displays the image
- *
- * @throw std::runtime_error when load fails (for example a memory
- * allocation issue, wrong rebin requested, etc.)
- */
-void LoadFITS::doLoadFiles(const std::vector<std::string> &paths,
- const std::string &outWSName, bool loadAsRectImg) {
- std::vector<FITSInfo> headers;
-
- doLoadHeaders(paths, headers);
-
- // No extension is set -> it's the standard format which we can parse.
- if (headers[0].numberOfAxis > 0)
- m_pixelCount += headers[0].axisPixelLengths[0];
-
- // Presumably 2 axis, but futureproofing.
- for (int i = 1; i < headers[0].numberOfAxis; ++i) {
- m_pixelCount *= headers[0].axisPixelLengths[i];
- }
-
- // Check consistency of m_rebin asap
- for (int i = 0; i < headers[0].numberOfAxis; ++i) {
- if (0 != (headers[0].axisPixelLengths[i] % m_rebin)) {
- throw std::runtime_error(
- "Cannot rebin this image in blocks of " +
- boost::lexical_cast<std::string>(m_rebin) + " x " +
- boost::lexical_cast<std::string>(m_rebin) +
- " pixels as requested because the size of dimension " +
- boost::lexical_cast<std::string>(i + 1) + " (" +
- boost::lexical_cast<std::string>(headers[0].axisPixelLengths[i]) +
- ") is not a multiple of the bin size.");
- }
- }
-
- MantidImage imageY(headers[0].axisPixelLengths[1],
- std::vector<double>(headers[0].axisPixelLengths[0]));
- MantidImage imageE(headers[0].axisPixelLengths[1],
- std::vector<double>(headers[0].axisPixelLengths[0]));
-
- size_t bytes = (headers[0].bitsPerPixel / 8) * m_pixelCount;
- std::vector<char> buffer;
- try {
- buffer.resize(bytes);
- } catch (std::exception &) {
- throw std::runtime_error(
- "Could not allocate enough memory to run when trying to allocate " +
- boost::lexical_cast<std::string>(bytes) + " bytes.");
- }
-
- // Create a group for these new workspaces, if the group already exists, add
- // to it.
- std::string groupName = outWSName;
-
- // This forms the name of the group
- m_baseName = getPropertyValue("OutputWorkspace") + "_";
-
- size_t fileNumberInGroup = 0;
- WorkspaceGroup_sptr wsGroup;
-
- if (!AnalysisDataService::Instance().doesExist(groupName)) {
- wsGroup = WorkspaceGroup_sptr(new WorkspaceGroup());
- wsGroup->setTitle(groupName);
- } else {
- // Get the name of the latest file in group to start numbering from
- if (AnalysisDataService::Instance().doesExist(groupName))
- wsGroup =
- AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(groupName);
-
- std::string latestName = wsGroup->getNames().back();
- // Set next file number
- fileNumberInGroup = fetchNumber(latestName) + 1;
- }
-
- size_t totalWS = headers.size();
- // Create a progress reporting object
- API::Progress progress(this, 0, 1, totalWS + 1);
- progress.report(0, "Loading file(s) into workspace(s)");
-
- // Create first workspace (with instrument definition). This is also used as
- // a template for creating others
- Workspace2D_sptr latestWS;
- latestWS = makeWorkspace(headers[0], fileNumberInGroup, buffer, imageY,
- imageE, latestWS, loadAsRectImg);
- progress.report(1, "First file loaded.");
-
- std::vector<Workspace2D_sptr> wsOrdered(totalWS);
- wsOrdered[0] = latestWS;
-
- if (isInstrOtherThanIMAT(headers[0])) {
- // For now we assume IMAT except when specific headers are found by
- // isInstrOtherThanIMAT()
- //
- // TODO: do this conditional on INSTR='IMAT' when we have proper IMAT .fits
- // files
- try {
- IAlgorithm_sptr loadInst = createChildAlgorithm("LoadInstrument");
- std::string directoryName =
- Kernel::ConfigService::Instance().getInstrumentDirectory();
- directoryName = directoryName + "/IMAT_Definition.xml";
- loadInst->setPropertyValue("Filename", directoryName);
- loadInst->setProperty<MatrixWorkspace_sptr>(
- "Workspace", boost::dynamic_pointer_cast<MatrixWorkspace>(latestWS));
- loadInst->execute();
- } catch (std::exception &ex) {
- g_log.information("Cannot load the instrument definition. " +
- std::string(ex.what()));
- }
- }
-
- // don't feel tempted to parallelize this loop as it is - it uses the same
- // imageY and imageE buffers for all the workspaces
- for (int64_t i = 1; i < static_cast<int64_t>(totalWS); ++i) {
- latestWS = makeWorkspace(headers[i], fileNumberInGroup, buffer, imageY,
- imageE, latestWS, loadAsRectImg);
- wsOrdered[i] = latestWS;
- progress.report("Loaded file " + boost::lexical_cast<std::string>(i + 1) +
- " of " + boost::lexical_cast<std::string>(totalWS));
- }
-
- // Add to group - done here to maintain sequence
- for (size_t i = 0; i < wsOrdered.size(); ++i) {
- wsGroup->addWorkspace(wsOrdered[i]);
- }
-
- setProperty("OutputWorkspace", wsGroup);
+ doLoadFiles(paths, outWSName, loadAsRectImg, binSize, noiseThresh);
}
/**
@@ -383,9 +220,9 @@ void LoadFITS::doLoadHeaders(const std::vector<std::string> &paths,
headers[i].axisPixelLengths.push_back(boost::lexical_cast<size_t>(
headers[i].headerKeys[m_headerAxisNameKeys[j]]));
// only debug level, when loading multiple files this is very verbose
- g_log.debug()
- << "Found axis length header entry: " << m_headerAxisNameKeys[j]
- << " = " << headers[i].axisPixelLengths.back() << std::endl;
+ g_log.debug() << "Found axis length header entry: "
+ << m_headerAxisNameKeys[j] << " = "
+ << headers[i].axisPixelLengths.back() << std::endl;
}
// Various extensions to the FITS format are used elsewhere, and
@@ -459,6 +296,210 @@ void LoadFITS::doLoadHeaders(const std::vector<std::string> &paths,
}
}
+/**
+ * Checks that a FITS header (once loaded) is valid/supported:
+ * standard (no extension to FITS), and has two axis with the expected
+ * dimensions.
+ *
+ * @param hdr FITS header struct loaded from a file - to check
+ *
+ * @param hdrFirst FITS header struct loaded from a (first) reference file -
+ *to
+ * compare against
+ *
+ * @throws std::exception if there's any issue or unsupported entry in the
+ * header
+ */
+void LoadFITS::headerSanityCheck(const FITSInfo &hdr,
+ const FITSInfo &hdrFirst) {
+ bool valid = true;
+ if (hdr.extension != "") {
+ valid = false;
+ g_log.error() << "File " << hdr.filePath
+ << ": extensions found in the header." << std::endl;
+ }
+ if (hdr.numberOfAxis != 2) {
+ valid = false;
+ g_log.error() << "File " << hdr.filePath
+ << ": the number of axes is not 2 but: " << hdr.numberOfAxis
+ << std::endl;
+ }
+
+ // Test current item has same axis values as first item.
+ if (hdr.axisPixelLengths[0] != hdrFirst.axisPixelLengths[0]) {
+ valid = false;
+ g_log.error() << "File " << hdr.filePath
+ << ": the number of pixels in the first dimension differs "
+ "from the first file loaded (" << hdrFirst.filePath
+ << "): " << hdr.axisPixelLengths[0]
+ << " != " << hdrFirst.axisPixelLengths[0] << std::endl;
+ }
+ if (hdr.axisPixelLengths[1] != hdrFirst.axisPixelLengths[1]) {
+ valid = false;
+ g_log.error() << "File " << hdr.filePath
+ << ": the number of pixels in the second dimension differs"
+ "from the first file loaded (" << hdrFirst.filePath
+ << "): " << hdr.axisPixelLengths[0]
+ << " != " << hdrFirst.axisPixelLengths[0] << std::endl;
+ }
+
+ // Check the format is correct and create the Workspace
+ if (!valid) {
+ // Invalid files, record error
+ throw std::runtime_error(
+ "An issue has been found in the header of this FITS file: " +
+ hdr.filePath +
+ ". This algorithm currently doesn't support FITS files with "
+ "non-standard extensions, more than two axis "
+ "of data, or has detected that all the files are "
+ "not similar.");
+ }
+}
+
+/**
+ * Create FITS file information for each file selected. Loads headers
+ * and data from the files and creates and fills the output
+ * workspace(s).
+ *
+ * @param paths File names as given in the algorithm input property
+ *
+ * @param outWSName name of the output (group) workspace to create
+ *
+ * @param loadAsRectImg Load files with 1 spectrum per row and 1 bin
+ * per column, so a color fill plot displays the image
+ *
+ * @param binSize size to rebin (1 == no re-bin == default)
+ *
+ * @param noiseThresh threshold for noise filtering
+ *
+ * @throw std::runtime_error when load fails (for example a memory
+ * allocation issue, wrong rebin requested, etc.)
+ */
+void LoadFITS::doLoadFiles(const std::vector<std::string> &paths,
+ const std::string &outWSName, bool loadAsRectImg,
+ int binSize, double noiseThresh) {
+ std::vector<FITSInfo> headers;
+
+ doLoadHeaders(paths, headers);
+
+ // No extension is set -> it's the standard format which we can parse.
+ if (headers[0].numberOfAxis > 0)
+ m_pixelCount += headers[0].axisPixelLengths[0];
+
+ // Presumably 2 axis, but futureproofing.
+ for (int i = 1; i < headers[0].numberOfAxis; ++i) {
+ m_pixelCount *= headers[0].axisPixelLengths[i];
+ }
+
+ // Check consistency of binSize asap
+ for (int i = 0; i < headers[0].numberOfAxis; ++i) {
+ if (0 != (headers[0].axisPixelLengths[i] % binSize)) {
+ throw std::runtime_error(
+ "Cannot rebin this image in blocks of " +
+ boost::lexical_cast<std::string>(binSize) + " x " +
+ boost::lexical_cast<std::string>(binSize) +
+ " pixels as requested because the size of dimension " +
+ boost::lexical_cast<std::string>(i + 1) + " (" +
+ boost::lexical_cast<std::string>(headers[0].axisPixelLengths[i]) +
+ ") is not a multiple of the bin size.");
+ }
+ }
+
+ MantidImage imageY(headers[0].axisPixelLengths[1],
+ std::vector<double>(headers[0].axisPixelLengths[0]));
+ MantidImage imageE(headers[0].axisPixelLengths[1],
+ std::vector<double>(headers[0].axisPixelLengths[0]));
+
+ size_t bytes = (headers[0].bitsPerPixel / 8) * m_pixelCount;
+ std::vector<char> buffer;
+ try {
+ buffer.resize(bytes);
+ } catch (std::exception &) {
+ throw std::runtime_error(
+ "Could not allocate enough memory to run when trying to allocate " +
+ boost::lexical_cast<std::string>(bytes) + " bytes.");
+ }
+
+ // Create a group for these new workspaces, if the group already exists, add
+ // to it.
+ std::string groupName = outWSName;
+
+ // This forms the name of the group
+ m_baseName = getPropertyValue("OutputWorkspace") + "_";
+
+ size_t fileNumberInGroup = 0;
+ WorkspaceGroup_sptr wsGroup;
+
+ if (!AnalysisDataService::Instance().doesExist(groupName)) {
+ wsGroup = WorkspaceGroup_sptr(new WorkspaceGroup());
+ wsGroup->setTitle(groupName);
+ } else {
+ // Get the name of the latest file in group to start numbering from
+ if (AnalysisDataService::Instance().doesExist(groupName))
+ wsGroup =
+ AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(groupName);
+
+ std::string latestName = wsGroup->getNames().back();
+ // Set next file number
+ fileNumberInGroup = fetchNumber(latestName) + 1;
+ }
+
+ size_t totalWS = headers.size();
+ // Create a progress reporting object
+ API::Progress progress(this, 0, 1, totalWS + 1);
+ progress.report(0, "Loading file(s) into workspace(s)");
+
+ // Create first workspace (with instrument definition). This is also used as
+ // a template for creating others
+ Workspace2D_sptr latestWS;
+ latestWS =
+ makeWorkspace(headers[0], fileNumberInGroup, buffer, imageY, imageE,
+ latestWS, loadAsRectImg, binSize, noiseThresh);
+ progress.report(1, "First file loaded.");
+
+ std::vector<Workspace2D_sptr> wsOrdered(totalWS);
+ wsOrdered[0] = latestWS;
+
+ if (isInstrOtherThanIMAT(headers[0])) {
+ // For now we assume IMAT except when specific headers are found by
+ // isInstrOtherThanIMAT()
+ //
+ // TODO: do this conditional on INSTR='IMAT' when we have proper IMAT .fits
+ // files
+ try {
+ IAlgorithm_sptr loadInst = createChildAlgorithm("LoadInstrument");
+ std::string directoryName =
+ Kernel::ConfigService::Instance().getInstrumentDirectory();
+ directoryName = directoryName + "/IMAT_Definition.xml";
+ loadInst->setPropertyValue("Filename", directoryName);
+ loadInst->setProperty<MatrixWorkspace_sptr>(
+ "Workspace", boost::dynamic_pointer_cast<MatrixWorkspace>(latestWS));
+ loadInst->execute();
+ } catch (std::exception &ex) {
+ g_log.information("Cannot load the instrument definition. " +
+ std::string(ex.what()));
+ }
+ }
+
+ // don't feel tempted to parallelize this loop as it is - it uses the same
+ // imageY and imageE buffers for all the workspaces
+ for (int64_t i = 1; i < static_cast<int64_t>(totalWS); ++i) {
+ latestWS =
+ makeWorkspace(headers[i], fileNumberInGroup, buffer, imageY, imageE,
+ latestWS, loadAsRectImg, binSize, noiseThresh);
+ wsOrdered[i] = latestWS;
+ progress.report("Loaded file " + boost::lexical_cast<std::string>(i + 1) +
+ " of " + boost::lexical_cast<std::string>(totalWS));
+ }
+
+ // Add to group - done here to maintain sequence
+ for (size_t i = 0; i < wsOrdered.size(); ++i) {
+ wsGroup->addWorkspace(wsOrdered[i]);
+ }
+
+ setProperty("OutputWorkspace", wsGroup);
+}
+
/**
* Read a single files header and populate an object with the information.
*
@@ -542,13 +583,17 @@ void LoadFITS::parseHeader(FITSInfo &headerInfo) {
* spectrum per row and one bin per column, instead of the (default)
* as many spectra as pixels.
*
+ * @param binSize size to rebin (1 == no re-bin == default)
+ *
+ * @param noiseThresh threshold for noise filtering
+ *
* @returns A newly created Workspace2D, as a shared pointer
*/
Workspace2D_sptr
LoadFITS::makeWorkspace(const FITSInfo &fileInfo, size_t &newFileNumber,
std::vector<char> &buffer, MantidImage &imageY,
MantidImage &imageE, const Workspace2D_sptr parent,
- bool loadAsRectImg) {
+ bool loadAsRectImg, int binSize, double noiseThresh) {
std::string currNumberS = padZeros(newFileNumber, g_DIGIT_SIZE_APPEND);
++newFileNumber;
@@ -558,7 +603,7 @@ LoadFITS::makeWorkspace(const FITSInfo &fileInfo, size_t &newFileNumber,
Workspace2D_sptr ws;
if (!parent) {
if (!loadAsRectImg) {
- size_t finalPixelCount = m_pixelCount / m_rebin * m_rebin;
+ size_t finalPixelCount = m_pixelCount / binSize * binSize;
ws = boost::dynamic_pointer_cast<Workspace2D>(
WorkspaceFactory::Instance().create("Workspace2D", finalPixelCount, 2,
1));
@@ -566,10 +611,10 @@ LoadFITS::makeWorkspace(const FITSInfo &fileInfo, size_t &newFileNumber,
ws = boost::dynamic_pointer_cast<Workspace2D>(
WorkspaceFactory::Instance().create(
"Workspace2D",
- fileInfo.axisPixelLengths[1] / m_rebin, // one bin per column
- fileInfo.axisPixelLengths[0] / m_rebin +
+ fileInfo.axisPixelLengths[1] / binSize, // one bin per column
+ fileInfo.axisPixelLengths[0] / binSize +
1, // one spectrum per row
- fileInfo.axisPixelLengths[0] / m_rebin));
+ fileInfo.axisPixelLengths[0] / binSize));
}
} else {
ws = boost::dynamic_pointer_cast<Workspace2D>(
@@ -582,27 +627,27 @@ LoadFITS::makeWorkspace(const FITSInfo &fileInfo, size_t &newFileNumber,
double cmpp = 1; // cm per pixel == bin width
if (0.0 != cm_1)
cmpp /= cm_1;
- cmpp *= static_cast<double>(m_rebin);
+ cmpp *= static_cast<double>(binSize);
- if (loadAsRectImg && 1 == m_rebin) {
+ if (loadAsRectImg && 1 == binSize) {
// set data directly into workspace
readDataToWorkspace(fileInfo, cmpp, ws, buffer);
} else {
readDataToImgs(fileInfo, imageY, imageE, buffer);
- doFilterNoise(m_noiseThresh, imageY, imageE);
+ doFilterNoise(noiseThresh, imageY, imageE);
// Note this can change the sizes of the images and the number of pixels
- if (1 == m_rebin) {
+ if (1 == binSize) {
ws->setImageYAndE(imageY, imageE, 0, loadAsRectImg, cmpp,
false /* no parallel load */);
} else {
- MantidImage rebinnedY(imageY.size() / m_rebin,
- std::vector<double>(imageY[0].size() / m_rebin));
- MantidImage rebinnedE(imageE.size() / m_rebin,
- std::vector<double>(imageE[0].size() / m_rebin));
+ MantidImage rebinnedY(imageY.size() / binSize,
+ std::vector<double>(imageY[0].size() / binSize));
+ MantidImage rebinnedE(imageE.size() / binSize,
+ std::vector<double>(imageE[0].size() / binSize));
- doRebin(m_rebin, imageY, imageE, rebinnedY, rebinnedE);
+ doRebin(binSize, imageY, imageE, rebinnedY, rebinnedE);
ws->setImageYAndE(rebinnedY, rebinnedE, 0, loadAsRectImg, cmpp,
false /* no parallel load */);
}
@@ -610,19 +655,33 @@ LoadFITS::makeWorkspace(const FITSInfo &fileInfo, size_t &newFileNumber,
ws->setTitle(Poco::Path(fileInfo.filePath).getFileName());
- addAxesInfoAndLogs(ws, loadAsRectImg, fileInfo, cmpp);
+ addAxesInfoAndLogs(ws, loadAsRectImg, fileInfo, binSize, cmpp);
return ws;
}
/**
+ * Add information to the workspace being loaded: labels, units, logs related to
+ * the image size, etc.
+ *
+ * @param ws workspace to manipulate
*
+ * @param loadAsRectImg if true, the workspace has one spectrum per
+ * row and one bin per column
+ *
+ * @param fileInfo information for the current file
+ *
+ * @param binSize size to rebin (1 == no re-bin == default)
+ *
+ * @param cmpp centimeters per pixel (already taking into account
+ * possible rebinning)
*/
void LoadFITS::addAxesInfoAndLogs(Workspace2D_sptr ws, bool loadAsRectImg,
- const FITSInfo &fileInfo, double cmpp) {
+ const FITSInfo &fileInfo, int binSize,
+ double cmpp) {
// add axes
- size_t width = fileInfo.axisPixelLengths[0] / m_rebin;
- size_t height = fileInfo.axisPixelLengths[1] / m_rebin;
+ size_t width = fileInfo.axisPixelLengths[0] / binSize;
+ size_t height = fileInfo.axisPixelLengths[1] / binSize;
if (loadAsRectImg) {
// width/X axis
auto axw = new Mantid::API::NumericAxis(width + 1);
@@ -944,66 +1003,6 @@ void LoadFITS::doRebin(size_t rebin, MantidImage &imageY, MantidImage &imageE,
}
}
-/**
- * Checks that a FITS header (once loaded) is valid/supported:
- * standard (no extension to FITS), and has two axis with the expected
- * dimensions.
- *
- * @param hdr FITS header struct loaded from a file - to check
- *
- * @param hdrFirst FITS header struct loaded from a (first) reference file -
- *to
- * compare against
- *
- * @throws std::exception if there's any issue or unsupported entry in the
- * header
- */
-void LoadFITS::headerSanityCheck(const FITSInfo &hdr,
- const FITSInfo &hdrFirst) {
- bool valid = true;
- if (hdr.extension != "") {
- valid = false;
- g_log.error() << "File " << hdr.filePath
- << ": extensions found in the header." << std::endl;
- }
- if (hdr.numberOfAxis != 2) {
- valid = false;
- g_log.error() << "File " << hdr.filePath
- << ": the number of axes is not 2 but: " << hdr.numberOfAxis
- << std::endl;
- }
-
- // Test current item has same axis values as first item.
- if (hdr.axisPixelLengths[0] != hdrFirst.axisPixelLengths[0]) {
- valid = false;
- g_log.error() << "File " << hdr.filePath
- << ": the number of pixels in the first dimension differs "
- "from the first file loaded (" << hdrFirst.filePath
- << "): " << hdr.axisPixelLengths[0]
- << " != " << hdrFirst.axisPixelLengths[0] << std::endl;
- }
- if (hdr.axisPixelLengths[1] != hdrFirst.axisPixelLengths[1]) {
- valid = false;
- g_log.error() << "File " << hdr.filePath
- << ": the number of pixels in the second dimension differs"
- "from the first file loaded (" << hdrFirst.filePath
- << "): " << hdr.axisPixelLengths[0]
- << " != " << hdrFirst.axisPixelLengths[0] << std::endl;
- }
-
- // Check the format is correct and create the Workspace
- if (!valid) {
- // Invalid files, record error
- throw std::runtime_error(
- "An issue has been found in the header of this FITS file: " +
- hdr.filePath +
- ". This algorithm currently doesn't support FITS files with "
- "non-standard extensions, more than two axis "
- "of data, or has detected that all the files are "
- "not similar.");
- }
-}
-
/**
* Looks for headers used by specific instruments/cameras, or finds if
* the instrument does not appear to be IMAT, which is the only one
@@ -1030,7 +1029,7 @@ bool LoadFITS::isInstrOtherThanIMAT(FITSInfo &hdr) {
<< it->second
<< ". This file seems to come from a Starlight camera, "
"as used for calibration of the instruments HiFi and EMU (and"
- "possibly others). Not "
+ "possibly others). Note: not "
"loading instrument definition." << std::endl;
}
@@ -1038,43 +1037,28 @@ bool LoadFITS::isInstrOtherThanIMAT(FITSInfo &hdr) {
}
/**
- * Returns the trailing number from a string minus leading 0's (so 25 from
- * workspace_00025).
- *
- * @param name string with a numerical suffix
- *
- * @returns A numerical representation of the string minus leading characters
- * and leading 0's
+ * Sets several keyword names with default (and standard) values. You
+ * don't want to change these unless you want to break compatibility
+ * with the FITS standard.
*/
-size_t LoadFITS::fetchNumber(const std::string &name) {
- std::string tmpStr = "";
- for (auto it = name.end() - 1; isdigit(*it); --it) {
- tmpStr.insert(0, 1, *it);
- }
- while (tmpStr.length() > 0 && tmpStr[0] == '0') {
- tmpStr.erase(tmpStr.begin());
- }
- return (tmpStr.length() > 0) ? boost::lexical_cast<size_t>(tmpStr) : 0;
-}
+void LoadFITS::setupDefaultKeywordNames() {
+ // Inits all the absolutely necessary keywords
+ // standard headers (If SIMPLE=T)
+ m_headerScaleKey = "BSCALE";
+ m_headerOffsetKey = "BZERO";
+ m_headerBitDepthKey = "BITPIX";
+ m_headerImageKeyKey = "IMAGE_TYPE"; // This is a "HIERARCH Image/Type= "
+ m_headerRotationKey = "ROTATION";
-/**
- * Adds 0's to the front of a number to create a string of size
- * totalDigitCount including number
- *
- * @param number input number to add padding to
- *
- * @param totalDigitCount width of the resulting string with 0s followed by
- * number
- *
- * @return A string with the 0-padded number
- */
-std::string LoadFITS::padZeros(const size_t number,
- const size_t totalDigitCount) {
- std::ostringstream ss;
- ss << std::setw(static_cast<int>(totalDigitCount)) << std::setfill('0')
- << static_cast<int>(number);
+ m_headerNAxisNameKey = "NAXIS";
+ m_headerAxisNameKeys.push_back("NAXIS1");
+ m_headerAxisNameKeys.push_back("NAXIS2");
- return ss.str();
+ m_mapFile = "";
+
+ // extensions
+ m_sampleRotation = "HIERARCH Sample/Tomo_Angle";
+ m_imageType = "HIERARCH Image/Type";
}
/**
@@ -1125,5 +1109,44 @@ void LoadFITS::mapHeaderKeys() {
}
}
+/**
+ * Returns the trailing number from a string minus leading 0's (so 25 from
+ * workspace_00025).
+ *
+ * @param name string with a numerical suffix
+ *
+ * @returns A numerical representation of the string minus leading characters
+ * and leading 0's
+ */
+size_t LoadFITS::fetchNumber(const std::string &name) {
+ std::string tmpStr = "";
+ for (auto it = name.end() - 1; isdigit(*it); --it) {
+ tmpStr.insert(0, 1, *it);
+ }
+ while (tmpStr.length() > 0 && tmpStr[0] == '0') {
+ tmpStr.erase(tmpStr.begin());
+ }
+ return (tmpStr.length() > 0) ? boost::lexical_cast<size_t>(tmpStr) : 0;
+}
+
+/**
+ * Adds 0's to the front of a number to create a string of size
+ * totalDigitCount including number
+ *
+ * @param number input number to add padding to
+ *
+ * @param totalDigitCount width of the resulting string with 0s followed by
+ * number
+ *
+ * @return A string with the 0-padded number
+ */
+std::string LoadFITS::padZeros(const size_t number,
+ const size_t totalDigitCount) {
+ std::ostringstream ss;
+ ss << std::setw(static_cast<int>(totalDigitCount)) << std::setfill('0')
+ << static_cast<int>(number);
+
+ return ss.str();
+}
} // namespace DataHandling
} // namespace Mantid