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metadata_table.cpp
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metadata_table.cpp
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/***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* This complete copyright notice must be included in any revised version of the
* source code. Additional authorship citations may be added, but existing
* author citations must be preserved.
***************************************************************************/
/***************************************************************************
*
* Authors: J.R. Bilbao-Castro (jrbcast@ace.ual.es)
*
* Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
* 02111-1307 USA
*
* All comments concerning this program package may be sent to the
* e-mail address 'xmipp@cnb.csic.es'
***************************************************************************/
#include "src/metadata_table.h"
#include "src/metadata_label.h"
MetaDataTable::MetaDataTable()
: objects(0),
label2offset(EMDL_LAST_LABEL, -1),
current_objectID(0),
doubleLabels(0),
intLabels(0),
boolLabels(0),
stringLabels(0),
doubleVectorLabels(0),
unknownLabels(0),
isList(false),
name(""),
comment(""),
version(CURRENT_MDT_VERSION),
activeLabels(0)
{
}
MetaDataTable::MetaDataTable(const MetaDataTable &MD)
: objects(MD.objects.size()),
label2offset(MD.label2offset),
unknownLabelPosition2Offset(MD.unknownLabelPosition2Offset),
unknownLabelNames(MD.unknownLabelNames),
current_objectID(0),
doubleLabels(MD.doubleLabels),
intLabels(MD.intLabels),
boolLabels(MD.boolLabels),
stringLabels(MD.stringLabels),
doubleVectorLabels(MD.doubleVectorLabels),
unknownLabels(MD.unknownLabels),
isList(MD.isList),
name(MD.name),
comment(MD.comment),
version(MD.version),
activeLabels(MD.activeLabels)
{
for (size_t idx = 0; idx < MD.objects.size(); idx++)
{
objects[idx] = new MetaDataContainer(*(MD.objects[idx]));
objects[idx]->table = this;
}
}
MetaDataTable& MetaDataTable::operator = (const MetaDataTable &MD)
{
if (this != &MD)
{
clear();
objects.resize(MD.objects.size());
label2offset = MD.label2offset;
unknownLabelPosition2Offset = MD.unknownLabelPosition2Offset;
unknownLabelNames = MD.unknownLabelNames;
current_objectID = 0;
doubleLabels = MD.doubleLabels;
intLabels = MD.intLabels;
boolLabels = MD.boolLabels;
stringLabels = MD.stringLabels;
doubleVectorLabels = MD.doubleVectorLabels;
unknownLabels = MD.unknownLabels;
isList = MD.isList;
name = MD.name;
comment = MD.comment;
version = MD.version;
activeLabels = MD.activeLabels;
for (long int idx = 0; idx < MD.objects.size(); idx++)
{
objects[idx] = new MetaDataContainer(this, MD.objects[idx]);
objects[idx]->table = this;
}
}
return *this;
}
void MetaDataTable::setIsList(bool is_list)
{
isList = is_list;
}
MetaDataTable::~MetaDataTable()
{
for (long i = 0; i < objects.size(); i++)
{
delete objects[i];
}
}
bool MetaDataTable::isEmpty() const
{
return (objects.size()==0);
}
size_t MetaDataTable::numberOfObjects() const
{
return objects.size();
}
void MetaDataTable::clear()
{
for (long i = 0; i < objects.size(); i++)
{
delete objects[i];
}
objects.clear();
label2offset = std::vector<long>(EMDL_LAST_LABEL, -1);
current_objectID = 0;
unknownLabelPosition2Offset.clear();
unknownLabelNames.clear();
doubleLabels = 0;
intLabels = 0;
boolLabels = 0;
stringLabels = 0;
unknownLabels = 0;
isList = false;
name = "";
comment = "";
version = CURRENT_MDT_VERSION;
activeLabels.clear();
}
void MetaDataTable::setComment(const std::string newComment)
{
comment = newComment;
}
std::string MetaDataTable::getComment() const
{
return comment;
}
bool MetaDataTable::containsComment() const
{
return (comment != std::string(""));
}
void MetaDataTable::setName(const std::string newName)
{
name = newName;
}
std::string MetaDataTable::getName() const
{
return name;
}
void MetaDataTable::setVersion(int v)
{
version = v;
}
int MetaDataTable::getVersion() const
{
return version;
}
int MetaDataTable::getCurrentVersion()
{
return CURRENT_MDT_VERSION;
}
std::string MetaDataTable::getUnknownLabelNameAt(int i) const
{
if (activeLabels[i] != EMDL_UNKNOWN_LABEL)
REPORT_ERROR("MetaDataTable::getUnknownLabelNameAt(): the requested column is not an unknown label.");
return unknownLabelNames[unknownLabelPosition2Offset[i]];
}
bool MetaDataTable::getValueToString(EMDLabel label, std::string &value, long objectID, bool escape) const
{
// SHWS 18jul2018: this function previously had a stringstream, but it greatly slowed down
// writing of large STAR files in some strange circumstances (with large data.star
// and model.star files in refinement)
// Therefore replaced the strstream with faster snprintf
//
// JZ 9aug2018: still using a stringstream for vector<double> fields
// => Avoid vector-valued columns in particle star-files.
char buffer[14];
if (EMDL::isString(label))
{
if (!getValue(label, value, objectID))
return false;
if (escape)
escapeStringForSTAR(value);
return true;
}
else
{
if (EMDL::isDouble(label))
{
double v;
if(!getValue(label, v, objectID)) return false;
if ((ABS(v) > 0. && ABS(v) < 0.001) || ABS(v) > 100000.)
{
if (v < 0.)
{
snprintf(buffer,13, "%12.5e", v);
}
else
{
snprintf(buffer,13, "%12.6e", v);
}
}
else
{
if (v < 0.)
{
snprintf(buffer,13, "%12.5f", v);
}
else
{
snprintf(buffer,13, "%12.6f", v);
}
}
}
else if (EMDL::isInt(label))
{
long v;
if (!getValue(label, v, objectID)) return false;
snprintf(buffer,13, "%12ld", v);
}
else if (EMDL::isBool(label))
{
bool v;
if (!getValue(label, v, objectID)) return false;
snprintf(buffer,13, "%12d", (int)v);
}
else if (EMDL::isDoubleVector(label))
{
std::vector<double> v;
getValue(label, v, objectID);
if (v.size() == 0)
{
value = "[]";
}
else
{
std::stringstream sts;
sts << std::setprecision(12);
sts << '[';
for (int i = 0; i < v.size()-1; i++)
{
sts << v[i] << ',';
}
sts << v[v.size()-1] << ']';
value = sts.str();
}
return true;
}
std::string tt(buffer);
value = tt;
return true;
}
}
int MetaDataTable::getInt(EMDLabel label, long objectID) const
{
int out = 0;
getValue(label, out, objectID);
return out;
}
int MetaDataTable::getIntMinusOne(EMDLabel label, long objectID) const
{
return getInt(label, objectID) - 1;
}
RFLOAT MetaDataTable::getRfloat(EMDLabel label, long objectID) const
{
RFLOAT out = 0.f;
getValue(label, out, objectID);
return out;
}
RFLOAT MetaDataTable::getDouble(EMDLabel label, long objectID) const
{
return (double) getRfloat(label, objectID);
}
RFLOAT MetaDataTable::getAngleInRad(EMDLabel label, long objectID) const
{
return DEG2RAD(getDouble(label, objectID));
}
bool MetaDataTable::getBool(EMDLabel label, long objectID) const
{
bool out = false;
getValue(label, out, objectID);
return out;
}
std::string MetaDataTable::getString(EMDLabel label, long objectID) const
{
std::string out = "";
getValue(label, out, objectID);
return out;
}
std::vector<double> MetaDataTable::getDoubleVector(EMDLabel label, long objectID) const
{
std::vector<double> out(0);
getValue(label, out, objectID);
return out;
}
bool MetaDataTable::setUnknownValue(int labelPosition, const std::string &value)
{
long offset = unknownLabelPosition2Offset[labelPosition];
if (offset < 0) REPORT_ERROR("MetaDataTable::setValueFromString BUG: offset should not be negative here....");
if (offset > -1)
{
objects[current_objectID]->unknowns[offset] = value;
return true;
}
else
{
return false;
}
}
bool MetaDataTable::setValueFromString(
EMDLabel label, const std::string &value, long int objectID)
{
if (EMDL::isString(label))
{
return setValue(label, value, objectID);
}
else
{
std::istringstream i(value);
if (EMDL::isDouble(label))
{
double v;
i >> v;
return setValue(label, v, objectID);
}
else if (EMDL::isInt(label))
{
long v;
i >> v;
return setValue(label, v, objectID);
}
else if (EMDL::isBool(label))
{
bool v;
i >> v;
return setValue(label, v, objectID);
}
else if (EMDL::isDoubleVector(label))
{
std::vector<double> v;
v.reserve(32);
char* temp = new char[value.size()+1];
strcpy(temp, value.c_str());
char* token;
char* rest = temp;
while ((token = strtok_r(rest, "[,]", &rest)) != 0)
{
double d;
std::stringstream sts(token);
sts >> d;
v.push_back(d);
}
delete[] temp;
return setValue(label, v, objectID);
}
}
REPORT_ERROR("Logic error: should not happen");
return false;
}
// comparators used for sorting
struct MdDoubleComparator
{
MdDoubleComparator(long index) : index(index) {}
bool operator()(MetaDataContainer *lh, MetaDataContainer *rh) const
{
return lh->doubles[index] < rh->doubles[index];
}
long index;
};
struct MdIntComparator
{
MdIntComparator(long index) : index(index) {}
bool operator()(MetaDataContainer *lh, MetaDataContainer *rh) const
{
return lh->ints[index] < rh->ints[index];
}
long index;
};
struct MdStringComparator
{
MdStringComparator(long index) : index(index) {}
bool operator()(MetaDataContainer *lh, MetaDataContainer *rh) const
{
return lh->strings[index] < rh->strings[index];
}
long index;
};
struct MdStringAfterAtComparator
{
MdStringAfterAtComparator(long index) : index(index) {}
bool operator()(MetaDataContainer *lh, MetaDataContainer *rh) const
{
std::string slh = lh->strings[index];
std::string srh = rh->strings[index];
slh = slh.substr(slh.find("@")+1);
srh = srh.substr(srh.find("@")+1);
return slh < srh;
}
long index;
};
struct MdStringBeforeAtComparator
{
MdStringBeforeAtComparator(long index) : index(index) {}
bool operator()(MetaDataContainer *lh, MetaDataContainer *rh) const
{
std::string slh = lh->strings[index];
std::string srh = rh->strings[index];
slh = slh.substr(0, slh.find("@"));
srh = srh.substr(0, srh.find("@"));
std::stringstream stslh, stsrh;
stslh << slh;
stsrh << srh;
long ilh, irh;
stslh >> ilh;
stsrh >> irh;
return ilh < irh;
}
long index;
};
void MetaDataTable::sort(EMDLabel name, bool do_reverse, bool only_set_index, bool do_random)
{
if (do_random)
{
srand (time(NULL)); /* initialize random seed: */
}
else if (!EMDL::isNumber(name))
{
REPORT_ERROR("MetadataTable::sort%% ERROR: can only sorted numbers");
}
std::vector<std::pair<double,long int> > vp;
vp.reserve(objects.size());
long int i = 0;
FOR_ALL_OBJECTS_IN_METADATA_TABLE(*this)
{
double dval;
if (do_random)
{
dval = (double)rand();
}
else if (EMDL::isInt(name))
{
long val;
getValue(name, val);
dval = (double) val;
}
else // EMDL::isDouble(name)
{
getValue(name, dval);
}
vp.push_back(std::make_pair(dval, i));
i++;
}
std::sort(vp.begin(), vp.end());
if (do_reverse && !do_random)
std::reverse(vp.begin(), vp.end());
if (only_set_index)
{
// Add an extra column with the sorted position of each entry
for (long j = 0; j < vp.size(); j++)
{
(*this).setValue(EMDL_SORTED_IDX, j, vp[j].second);
}
}
else
{
// Change the actual order in the MetaDataTable
std::vector<MetaDataContainer*> objs(objects.size());
for (long j = 0; j < vp.size(); j++)
{
objs[j] = objects[vp[j].second];
}
objects = objs;
}
// reset pointer to the beginning of the table
firstObject();
}
void MetaDataTable::newSort(const EMDLabel label, bool do_reverse, bool do_sort_after_at, bool do_sort_before_at)
{
if (EMDL::isString(label))
{
if (do_sort_after_at)
{
std::stable_sort(objects.begin(), objects.end(),
MdStringAfterAtComparator(label2offset[label]));
}
else if (do_sort_before_at)
{
std::stable_sort(objects.begin(), objects.end(),
MdStringBeforeAtComparator(label2offset[label]));
}
else
{
std::stable_sort(objects.begin(), objects.end(), MdStringComparator(label2offset[label]));
}
}
else if (EMDL::isDouble(label))
{
std::stable_sort(objects.begin(), objects.end(), MdDoubleComparator(label2offset[label]));
}
else if (EMDL::isInt(label))
{
std::stable_sort(objects.begin(), objects.end(), MdIntComparator(label2offset[label]));
}
else
{
REPORT_ERROR("Cannot sort this label: " + EMDL::label2Str(label));
}
if (do_reverse)
{
std::reverse(objects.begin(), objects.end());
}
}
// Will be removed in 3.2
bool MetaDataTable::labelExists(EMDLabel name) const
{
return containsLabel(name);
}
bool MetaDataTable::containsLabel(const EMDLabel label, std::string unknownLabel) const
{
for (int i = 0; i < activeLabels.size(); i++)
{
if (activeLabels[i] == label &&
(label != EMDL_UNKNOWN_LABEL || getUnknownLabelNameAt(i) == unknownLabel))
return true;
}
return false;
}
std::vector<EMDLabel> MetaDataTable::getActiveLabels() const
{
return activeLabels;
}
void MetaDataTable::deactivateLabel(EMDLabel label, std::string unknownLabel)
{
for (int i = 0; i < activeLabels.size(); i++)
{
if (activeLabels[i] == label &&
(label != EMDL_UNKNOWN_LABEL || unknownLabelNames[unknownLabelPosition2Offset[i]] == unknownLabel))
{
activeLabels.erase(activeLabels.begin() + i);
unknownLabelPosition2Offset.erase(unknownLabelPosition2Offset.begin() + i);
if (label != EMDL_UNKNOWN_LABEL)
label2offset[label] = -1;
}
}
}
void MetaDataTable::addLabel(EMDLabel label, std::string unknownLabel)
{
if (label >= EMDL_LAST_LABEL)
REPORT_ERROR(std::string("MetaDataTable::addLabel: unrecognised label: ") + EMDL::label2Str(label));
if (label == EMDL_UNKNOWN_LABEL && unknownLabel == "")
REPORT_ERROR("MetaDataTable::addLabel: unknownLabel is empty");
if (label2offset[label] < 0 || label == EMDL_UNKNOWN_LABEL) // keep pushing the same unknown label...
{
long id;
if (EMDL::isDouble(label))
{
id = doubleLabels;
for (long i = 0; i < objects.size(); i++)
{
objects[i]->doubles.push_back(0);
}
doubleLabels++;
}
else if (EMDL::isInt(label))
{
id = intLabels;
for (long i = 0; i < objects.size(); i++)
{
objects[i]->ints.push_back(0);
}
intLabels++;
}
else if (EMDL::isBool(label))
{
id = boolLabels;
for (long i = 0; i < objects.size(); i++)
{
objects[i]->bools.push_back(false);
}
boolLabels++;
}
else if (EMDL::isString(label))
{
id = stringLabels;
for (long i = 0; i < objects.size(); i++)
{
objects[i]->strings.push_back("empty");
}
stringLabels++;
}
else if (EMDL::isDoubleVector(label))
{
id = doubleVectorLabels;
for (long i = 0; i < objects.size(); i++)
{
objects[i]->doubleVectors.push_back(std::vector<double>());
}
doubleVectorLabels++;
}
else if (EMDL::isUnknown(label))
{
id = unknownLabels;
for (long i = 0; i < objects.size(); i++)
{
objects[i]->unknowns.push_back("empty");
}
unknownLabelNames.push_back(unknownLabel);
unknownLabels++;
}
activeLabels.push_back(label);
unknownLabelPosition2Offset.push_back(EMDL::isUnknown(label) ? id : -1);
label2offset[label] = id;
}
}
void MetaDataTable::addMissingLabels(const MetaDataTable* mdt)
{
for (long i = 0; i < mdt->activeLabels.size(); i++)
{
EMDLabel l = mdt->activeLabels[i];
if (l == EMDL_UNKNOWN_LABEL)
{
std::string unknownLabel = mdt->getUnknownLabelNameAt(i);
if (!containsLabel(l, unknownLabel))
addLabel(l, unknownLabel);
}
else if (label2offset[l] < 0)
{
addLabel(l);
}
}
}
void MetaDataTable::append(const MetaDataTable& mdt)
{
if (activeLabels.size() == 0)
{
// If the current one is empty, add missing labels and append the new one:
addMissingLabels(&mdt);
}
else
{
// If the current one is not-empty, check all labels are the same before appending. Otherwise, raise error
if (!compareLabels(*this, mdt))
REPORT_ERROR("ERROR in appending metadata tables with not the same columns!");
}
// Now append
objects.reserve(objects.size() + mdt.numberOfObjects());
for (long i = 0; i < mdt.objects.size(); i++)
{
objects.push_back(new MetaDataContainer(
this, doubleLabels, intLabels, boolLabels, stringLabels, doubleVectorLabels, unknownLabels));
setObjectUnsafe(mdt.getObject(i), objects.size() - 1);
}
// reset pointer to the beginning of the table
firstObject();
}
MetaDataContainer* MetaDataTable::getObject(long objectID) const
{
if (objectID < 0) objectID = current_objectID;
checkObjectID(objectID, "MetaDataTable::getObject");
return objects[objectID];
}
void MetaDataTable::setObject(MetaDataContainer* data, long objectID)
{
if (objectID < 0) objectID = current_objectID;
checkObjectID(objectID, "MetaDataTable::setObject");
addMissingLabels(data->table);
setObjectUnsafe(data, objectID);
}
void MetaDataTable::setValuesOfDefinedLabels(MetaDataContainer* data, long objectID)
{
if (objectID < 0) objectID = current_objectID;
checkObjectID(objectID, "MetaDataTable::setValuesOfDefinedLabels");
setObjectUnsafe(data, objectID);
}
void MetaDataTable::reserve(size_t capacity)
{
objects.reserve(capacity);
}
void MetaDataTable::setObjectUnsafe(MetaDataContainer* data, long objectID)
{
MetaDataContainer* obj = objects[objectID];
for (long i = 0; i < data->table->activeLabels.size(); i++)
{
EMDLabel label = data->table->activeLabels[i];
if (label != EMDL_UNKNOWN_LABEL)
{
long myOff = label2offset[label];
long srcOff = data->table->label2offset[label];
if (myOff < 0) continue;
if (EMDL::isDouble(label))
{
obj->doubles[myOff] = data->doubles[srcOff];
}
else if (EMDL::isInt(label))
{
obj->ints[myOff] = data->ints[srcOff];
}
else if (EMDL::isBool(label))
{
obj->bools[myOff] = data->bools[srcOff];
}
else if (EMDL::isString(label))
{
obj->strings[myOff] = data->strings[srcOff];
}
else if (EMDL::isDoubleVector(label))
{
obj->doubleVectors[myOff] = data->doubleVectors[srcOff];
}
}
else
{
std::string unknownLabel = data->table->getUnknownLabelNameAt(i);
long srcOff = data->table->unknownLabelPosition2Offset[i];
long myOff = -1;
for (int j = 0; j < unknownLabelNames.size(); j++)
{
if (unknownLabelNames[j] == unknownLabel)
{
myOff = j;
break;
}
}
if (myOff < 0)
REPORT_ERROR("MetaDataTable::setObjectUnsafe: logic error. cannot find srcOff.");
obj->unknowns[myOff] = data->unknowns[srcOff];
}
}
}
void MetaDataTable::addObject()
{
objects.push_back(new MetaDataContainer(
this, doubleLabels, intLabels, boolLabels, stringLabels, doubleVectorLabels, unknownLabels));
current_objectID = objects.size()-1;
}
void MetaDataTable::addObject(MetaDataContainer* data)
{
objects.push_back(new MetaDataContainer(
this, doubleLabels, intLabels, boolLabels, stringLabels, doubleVectorLabels, unknownLabels));
setObject(data, objects.size()-1);
current_objectID = objects.size()-1;
}
void MetaDataTable::addValuesOfDefinedLabels(MetaDataContainer* data)
{
objects.push_back(new MetaDataContainer(
this, doubleLabels, intLabels, boolLabels, stringLabels, doubleVectorLabels, unknownLabels));
setValuesOfDefinedLabels(data, objects.size()-1);
current_objectID = objects.size()-1;
}
void MetaDataTable::removeObject(long objectID)
{
long i = (objectID < 0) ? current_objectID : objectID;
checkObjectID(i, "MetaDataTable::removeObject");
delete objects[i];
objects.erase(objects.begin() + i);
current_objectID = objects.size() - 1;
}
long int MetaDataTable::firstObject()
{
current_objectID = 0;
return 0;
}
long int MetaDataTable::nextObject()
{
current_objectID++;
if (current_objectID >= objects.size())
{
return NO_MORE_OBJECTS;
}
else
{
return current_objectID;
}
}
long int MetaDataTable::goToObject(long int objectID)
{
checkObjectID(objectID, "MetaDataTable::goToObject");
current_objectID = objectID;
return current_objectID;
}
long int MetaDataTable::readStarLoop(std::ifstream& in, bool do_only_count)
{
setIsList(false);
//Read column labels
int labelPosition = 0;
std::string line, token;
// First read all the column labels
while (getline(in, line, '\n'))
{
line = simplify(line);
// TODO: handle comments...
if (line[0] == '#' || line[0] == '\0' || line[0] == ';')
continue;
if (line[0] == '_') // label definition line
{
//Only take string from "_" until "#"
size_t pos0 = line.find("_");
size_t pos1 = line.find("#");
token = line.substr(pos0 + 1, pos1 - pos0 - 2);
EMDLabel label = EMDL::str2Label(token);
if (label == EMDL_UNDEFINED)
{
std::cerr << " + WARNING: will ignore (but maintain) values for the unknown label: " << token << std::endl;
label = EMDL_UNKNOWN_LABEL;
}
addLabel(label, token);
labelPosition++;
}
else // found first data line
{
break;
}
}