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Merge branch 'DOI-USGS:dev' into bugfix/jigsawAdjustedPtCorrections
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,7 +1,6 @@ | ||
| channels: | ||
| - conda-forge | ||
| - defaults | ||
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| dependencies: | ||
| - ale =0.10.0,<1 | ||
| - aom | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| Group = Keyword1 | ||
| Auto = 1 | ||
| InputKey = SpacecraftName | ||
| InputGroup = "IsisCube,Instrument" | ||
| InputPosition = (IsisCube, Instrument) | ||
| OutputName = Keyword1 | ||
| OutputPosition = (Group, SerialNumberKeywords) | ||
| Translation = (*, *) | ||
| End_Group | ||
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| Group = Keyword2 | ||
| Auto = 1 | ||
| InputKey = InstrumentId | ||
| InputGroup = "IsisCube,Instrument" | ||
| InputPosition = (IsisCube, Instrument) | ||
| OutputName = Keyword2 | ||
| OutputPosition = (Group, SerialNumberKeywords) | ||
| Translation = (*, *) | ||
| End_Group | ||
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| Group = Keyword3 | ||
| Auto = 1 | ||
| InputKey = EphemerisTime | ||
| InputGroup = "IsisCube,Instrument" | ||
| InputPosition = (IsisCube, Instrument) | ||
| OutputName = Keyword3 | ||
| OutputPosition = (Group, SerialNumberKeywords) | ||
| Translation = (*, *) | ||
| End_Group | ||
| End |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,218 @@ | ||
| /** This is free and unencumbered software released into the public domain. | ||
| The authors of ISIS do not claim copyright on the contents of this file. | ||
| For more details about the LICENSE terms and the AUTHORS, you will | ||
| find files of those names at the top level of this repository. **/ | ||
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| /* SPDX-License-Identifier: CC0-1.0 */ | ||
| #include "csv2table.h" | ||
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| #include <vector> | ||
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| #include <QRegularExpression> | ||
| #include <QString> | ||
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| #include "Cube.h" | ||
| #include "CSVReader.h" | ||
| #include "IException.h" | ||
| #include "IString.h" | ||
| #include "Pvl.h" | ||
| #include "PvlObject.h" | ||
| #include "Table.h" | ||
| #include "TableField.h" | ||
| #include "TableRecord.h" | ||
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| using namespace std; | ||
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| namespace Isis { | ||
| /** | ||
| * csminit a cube in an Application | ||
| * | ||
| * @param ui The Application UI | ||
| * @param(out) log The Pvl that attempted models will be logged to | ||
| */ | ||
| void csv2table(UserInterface &ui, Pvl *log) { | ||
| // Read the CSV file and get the header | ||
| QString csvFileName = ui.GetFileName("csv"); | ||
| CSVReader reader; | ||
| try { | ||
| reader = CSVReader(csvFileName, true); | ||
| } | ||
| catch(IException &e) { | ||
| QString msg = "Failed to read CSV file [" + csvFileName + "]."; | ||
| throw IException(e, IException::Io, msg, _FILEINFO_); | ||
| } | ||
| int numColumns = reader.columns(); | ||
| int numRows = reader.rows(); | ||
| if (numColumns < 1 || numRows < 1) { | ||
| QString msg = "CSV file does not have data.\nFile has [" + toString(numRows) + | ||
| "] rows and [" + toString(numColumns) +"] columns."; | ||
| throw IException(IException::User, msg, _FILEINFO_); | ||
| } | ||
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| std::vector<QString> fieldTypes; | ||
| ui.GetAsString("coltypes", fieldTypes); | ||
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| std::vector<TableField::Type> tableTypes; | ||
| if (fieldTypes.size() == 1 && fieldTypes[0] == "") { | ||
| for (int i = 0; i < numColumns; i++) { | ||
| tableTypes.push_back(TableField::Double); | ||
| } | ||
| } | ||
| else { | ||
| if (fieldTypes.size() == numColumns) { | ||
| for (QString type: fieldTypes) { | ||
| QString upper_type = type.toUpper(); | ||
| if (upper_type == "INTEGER") { | ||
| tableTypes.push_back(TableField::Type::Integer); | ||
| } | ||
| else if (upper_type == "DOUBLE") { | ||
| tableTypes.push_back(TableField::Type::Double); | ||
| } | ||
| else if (upper_type == "TEXT") { | ||
| tableTypes.push_back(TableField::Type::Text); | ||
| } | ||
| else if (upper_type == "REAL") { | ||
| tableTypes.push_back(TableField::Type::Real); | ||
| } | ||
| else { | ||
| QString msg = "Field [" + type + "] cannot be translated. Accepted types are " | ||
| "Integer, Double, Text, and Real"; | ||
| throw IException(IException::User, msg, _FILEINFO_); | ||
| } | ||
| } | ||
| } | ||
| else { | ||
| int numFields = fieldTypes.size(); | ||
| QString msg = "Number of fields provided does not equal the number of columns in the CSV. " | ||
| "Number of fields [" + toString(numFields) + | ||
| "] vs Number of Columns [" + toString(numColumns) + "]"; | ||
| throw IException(IException::User, msg, _FILEINFO_); | ||
| } | ||
| } | ||
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| CSVReader::CSVAxis header = reader.getHeader(); | ||
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| // Construct an empty table with the CSV header as field names | ||
| // Collect identical field names together, including those with (###) at the end, so a single | ||
| // table field with multiple values can be created. | ||
| TableRecord tableRow; | ||
| QRegularExpression rex(R"((?<name>\w+)(\((?<index>[0-9]*)\)|))"); | ||
| for (int columnIndex = 0; columnIndex < numColumns; columnIndex++) { | ||
| QRegularExpressionMatch match = rex.match(header[columnIndex]); | ||
| if (match.hasMatch()) { | ||
| QString name = match.captured("name"); | ||
| QString index = match.captured("index"); | ||
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| // If the next column header is different, create a field for this one | ||
| QRegularExpressionMatch nextMatch = (columnIndex<numColumns-1)?rex.match(header[columnIndex+1]):QRegularExpressionMatch(); | ||
| if ((columnIndex == numColumns-1) || (nextMatch.hasMatch() && (name != nextMatch.captured("name")))) { | ||
| TableField columnField(name, tableTypes[columnIndex], (index.length()>0)?(index.toInt()+1):1); | ||
| tableRow += columnField; | ||
| } | ||
| } | ||
| } | ||
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| QString tableName = ui.GetString("tablename"); | ||
| Table table(tableName, tableRow); | ||
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| // Fill the table from the csv | ||
| for (int rowIndex = 0; rowIndex < numRows; rowIndex++) { | ||
| CSVReader::CSVAxis csvRow = reader.getRow(rowIndex); | ||
| for (int columnIndex = 0, fieldIndex = 0; columnIndex < numColumns; ) { | ||
| if (tableRow[fieldIndex].size() == 1 || | ||
| tableRow[fieldIndex].isText()) { | ||
| switch(tableTypes[columnIndex]) { | ||
| case TableField::Type::Integer: | ||
| tableRow[fieldIndex] = toInt(csvRow[columnIndex++]); | ||
| break; | ||
| case TableField::Type::Double: | ||
| tableRow[fieldIndex] = toDouble(csvRow[columnIndex++]); | ||
| break; | ||
| case TableField::Type::Text: | ||
| tableRow[fieldIndex] = QString(csvRow[columnIndex++]); | ||
| break; | ||
| case TableField::Type::Real: | ||
| tableRow[fieldIndex] = (float)toDouble(csvRow[columnIndex++]); | ||
| break; | ||
| } | ||
| } | ||
| else { | ||
| std::vector<int> intVector; | ||
| std::vector<double> dblVector; | ||
| std::vector<float> realVector; | ||
| QString strMsg = "TableRecord can't handle list of Strings"; | ||
| switch(tableTypes[columnIndex]) { | ||
| case TableField::Type::Integer: | ||
| for (int arrayLen = 0; arrayLen < tableRow[fieldIndex].size(); arrayLen++) { | ||
| intVector.push_back(toInt(csvRow[columnIndex++])); | ||
| } | ||
| tableRow[fieldIndex] = intVector; | ||
| break; | ||
| case TableField::Type::Double: | ||
| for (int arrayLen = 0; arrayLen < tableRow[fieldIndex].size(); arrayLen++) { | ||
| dblVector.push_back(toDouble(csvRow[columnIndex++])); | ||
| } | ||
| tableRow[fieldIndex] = dblVector; | ||
| break; | ||
| case TableField::Type::Text: | ||
| throw IException(IException::User, strMsg, _FILEINFO_); | ||
| break; | ||
| case TableField::Type::Real: | ||
| for (int arrayLen = 0; arrayLen < tableRow[fieldIndex].size(); arrayLen++) { | ||
| realVector.push_back((float)toDouble(csvRow[columnIndex++])); | ||
| } | ||
| tableRow[fieldIndex] = realVector; | ||
| break; | ||
| } | ||
| intVector.clear(); | ||
| dblVector.clear(); | ||
| realVector.clear(); | ||
| } | ||
| fieldIndex++; | ||
| } | ||
| table += tableRow; | ||
| } | ||
|
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| // If a set of additional label keywords was given then add them to the table's pvl description | ||
| if (ui.WasEntered("label")) { | ||
| QString labelPvlFilename = ui.GetFileName("label"); | ||
| Pvl labelPvl; | ||
| try { | ||
| labelPvl.read(labelPvlFilename); | ||
| } | ||
| catch(IException &e) { | ||
| QString msg = "Failed to read PVL label file [" + labelPvlFilename + "]."; | ||
| throw IException(e, IException::Io, msg, _FILEINFO_); | ||
| } | ||
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| PvlObject &tableLabel = table.Label(); | ||
| for (int keyIndex = 0; keyIndex < labelPvl.keywords(); keyIndex++) { | ||
| tableLabel.addKeyword(labelPvl[keyIndex]); | ||
| } | ||
| } | ||
|
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| // Write the table to the cube | ||
| QString outCubeFileName(ui.GetCubeName("to")); | ||
| Cube outCube; | ||
| try { | ||
| outCube.open(outCubeFileName, "rw"); | ||
| } | ||
| catch(IException &e) { | ||
| QString msg = "Could not open output cube [" + outCubeFileName + "]."; | ||
| throw IException(e, IException::Io, msg, _FILEINFO_); | ||
| } | ||
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| try { | ||
| outCube.write(table); | ||
| } | ||
| catch(IException &e) { | ||
| QString msg = "Could not write output table [" + tableName + | ||
| "] to output cube [" + outCubeFileName + "]."; | ||
| throw IException(e, IException::Io, msg, _FILEINFO_); | ||
| } | ||
|
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| outCube.close(); | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| #ifndef csv2table_h | ||
| #define csv2table_h | ||
| /** This is free and unencumbered software released into the public domain. | ||
| The authors of ISIS do not claim copyright on the contents of this file. | ||
| For more details about the LICENSE terms and the AUTHORS, you will | ||
| find files of those names at the top level of this repository. **/ | ||
|
|
||
| /* SPDX-License-Identifier: CC0-1.0 */ | ||
|
|
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| #include "Pvl.h" | ||
| #include "UserInterface.h" | ||
|
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| namespace Isis { | ||
| extern void csv2table(UserInterface &ui, Pvl *log=nullptr); | ||
| } | ||
|
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| #endif |
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