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Update Read_and_Write_Excel.java #1

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5651882
Update Read_and_Write_Excel.java
antinos Feb 27, 2018
4736d42
v1.1.1 and v1.1.2 changes
antinos Nov 8, 2018
14e4428
v1.1.5
antinos Dec 1, 2019
857aac3
v1.1.6
antinos May 20, 2020
efcc6af
Install instr. changed for most up-to-date version
antinos May 20, 2020
a8c9050
Install instr. changed for most up-to-date version
antinos May 20, 2020
e64e56f
v1.1.7
antinos Sep 26, 2020
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14 changes: 9 additions & 5 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ The defaults can be overridden when calling the plugin from an ImageJ macro usin
## Macro Parameters
This version of the Read_and_Write_Excel plugin supports additional features which make it more flexible for usage in ImageJ macros. These are the supported parameters:
* `no_count_column`: Prevents the plugin from adding a "Count" column automatically.
* `stack_results` : Instructs the plugin to export data underneath pre-existing data in the Excel file, instead of adjacent to it.
* `file=`: The path to the excel file to use (uses the default desktop file otherwise)
* `sheet=`: Which sheet in the excel file to put the results in
* `dataset_label=`: The label to write in the cell above the data in the excel file
Expand All @@ -21,10 +22,13 @@ This version of the Read_and_Write_Excel plugin supports additional features whi
## Installation
The easiest way to install the plugin is to use Fiji's built-in updater:
1) Go to Help > Update...
2) Click "Manage update sites"
3) Click "Add update site"
4) Give the new update site a name, and use the URL `http://sites.imagej.net/Bkromhout/`
5) You should now see the plugin available in the updater.
2) Click "Manage update sites"<br/>
~~3) Click "Add update site"~~<br/>
3) Find 'ResultsToExcel' in the list of plugins and mark the check-box.<br/>
~~4) Give the new update site a name, and use the URL `http://sites.imagej.net/Bkromhout/`~~ (*does not host the most recent version currently*)<br/>
4) Close the "Manage update sites" window and click "Apply changes" in the Imagej Updater main window.<br/>
~~5) You should now see the plugin available in the updater.~~<br/>
5) Restart ImageJ.

If you can't do that for some reason, you should also be able to download the latest release, unzip it, and copy the plugin's JAR to the ImageJ plugins folder, and the JARs in the "jars" folder to ImageJ's "jars" folder.

Expand All @@ -46,4 +50,4 @@ print("Wrote 2");

run("Read and Write Excel", "file_mode=write_and_close");
print("Closed file");
```
```
130 changes: 109 additions & 21 deletions src/main/java/Read_and_Write_Excel.java
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Expand Up @@ -4,6 +4,7 @@
import ij.plugin.filter.Analyzer;
import org.apache.poi.openxml4j.exceptions.InvalidFormatException;
import org.apache.poi.ss.usermodel.*;
import org.apache.poi.ss.util.CellReference;
import org.apache.poi.ss.util.WorkbookUtil;
import org.apache.poi.xssf.usermodel.XSSFWorkbook;

Expand All @@ -12,6 +13,7 @@
import java.io.FileOutputStream;
import java.io.IOException;

/**version 1.1.7*/
public class Read_and_Write_Excel implements PlugIn {
private enum FileHandlingMode { OPEN_CLOSE, READ_OPEN, WRITE_CLOSE, QUEUE}

Expand All @@ -31,6 +33,8 @@ private enum FileHandlingMode { OPEN_CLOSE, READ_OPEN, WRITE_CLOSE, QUEUE}
private String filePath;
private String sheetName;
private String dataSetLabel;
private String importCell;
private boolean stackResults = false;
private boolean noCountColumn = false;
private FileHandlingMode fileHandlingMode = FileHandlingMode.OPEN_CLOSE;

Expand All @@ -57,6 +61,11 @@ public static void main(String[] args) {
debugOptions = "no_count_column dataset_label=[Test dataset label] sheet=[Sheet Name] file=[/Users/bkromhout/Desktop/Results File.xlsx]";
new Read_and_Write_Excel().run("");
debugOptions = "no_count_column file=[/path/to/Results File.xlsx]";
new Read_and_Write_Excel().run("");
debugOptions = "stack_results";
new Read_and_Write_Excel().run("");
debugOptions = "cell_ref=[A1]";
new Read_and_Write_Excel().run("");
}

public void run(String arg) {
Expand Down Expand Up @@ -97,17 +106,27 @@ public void run(String arg) {

// Get results, the number of columns and rows, the data, and the headings.
ResultsTable resultsTable = debugTable == null ? Analyzer.getResultsTable() : debugTable;
int numColumns = resultsTable.getLastColumn() + 1;
int numColumns = resultsTable.getHeadings().length;
int numRows = resultsTable.size();
String[] headers = resultsTable.getHeadings();
String[][] results = new String[numRows][numColumns];

// Loop over the results. We could use the getRowAsString(), but we'd just have to split it and parse it again,
// plus it could mess up if there are any empty cells...this is the most sensible in the end.
for (int row = 0; row < numRows; row++)
for (int col = 0; col < numColumns; col++)
results[row][col] = resultsTable.getStringValue(col, row);

for (int row = 0; row < numRows; row++){
//Continue with results loop, as described above.
for (int col = 0; col < numColumns; col++){
//Solution for handling empty column cells, which otherwise causes the plugin to fail.
if (resultsTable.columnExists(headers[col]) == true && headers[col] != "Label" && !resultsTable.getStringValue(headers[col], row).isEmpty() ){
results[row][col] = resultsTable.getStringValue(headers[col], row); //Column header reference issue. Passing int for some reason calls hidden values. Passing header string works.
} else if(headers[col] == "Label" && resultsTable.getLabel(row) != null && !resultsTable.getLabel(row).isEmpty()) {
results[row][col] = resultsTable.getLabel(row);
} else {
results[row][col] = " ";
}
}
}

// Figure out which holder to use.
ExcelHolder holderToUse = fileHolder;
if (fileHandlingMode == FileHandlingMode.OPEN_CLOSE) {
Expand Down Expand Up @@ -149,6 +168,70 @@ public void run(String arg) {
f.setBold(true);
boldStyle.setFont(f);

// Write the column header cells. If stackResults is chosen, then only write the header cells if they do not exist already. If an import cell reference is specified, then do not write the headers at all.
if(importCell == null) {
row = sheet.getRow(COLUMN_HEADER_ROW);
if (row == null) row = sheet.createRow(COLUMN_HEADER_ROW);
if (stackResults != true) {
for (int headerIdx = 0; headerIdx < (headers.length + idxAdj); headerIdx++) {
int cellCol = firstColIdx + headerIdx;
Cell colHeader = row.getCell(cellCol);
if (colHeader == null) colHeader = row.createCell(cellCol);
// Make sure we write the "Count" column header to the first column, if we want it.
if (cellCol == firstColIdx && !noCountColumn) colHeader.setCellValue("Count");
else colHeader.setCellValue(headers[headerIdx - idxAdj]);
colHeader.setCellStyle(boldStyle);
}
} else {
if (sheet.getRow(COLUMN_HEADER_ROW).getCell(0) == null){
for (int headerIdx = 0; headerIdx < (headers.length + idxAdj); headerIdx++) {
int cellCol = firstColIdx + headerIdx;
Cell colHeader = row.getCell(cellCol);
if (colHeader == null) colHeader = row.createCell(cellCol);
// Make sure we write the "Count" column header to the first column, if we want it.
if (cellCol == firstColIdx && !noCountColumn) colHeader.setCellValue("Count");
else colHeader.setCellValue(headers[headerIdx - idxAdj]);
colHeader.setCellStyle(boldStyle);
}
}
}
}

// Change the first column index to write data to, depending on stack_results status.
row = sheet.getRow(FIRST_DATA_ROW);
int firstDataRow = FIRST_DATA_ROW;
if (sheet.getLastRowNum()!=1 && stackResults == true) {
int lastColIdx = row.getLastCellNum()-1;
// getLastCellNum() will output -1 if the row does not contain any cells, so we handle that scenario here (check for -2 as we already took away 1 above)
if (lastColIdx == -2) {
//when the results table is empty the headings length is output as 0, so this must also be handled
if (headers.length == 0) {
lastColIdx = 0;
} else lastColIdx = headers.length-1+idxAdj;
}
int lastRowOfLastColIdx = FIRST_DATA_ROW;
Row rowL = sheet.getRow(lastRowOfLastColIdx);
Cell testCell = row.getCell(lastColIdx);
while (testCell != null){
lastRowOfLastColIdx++;
rowL = sheet.getRow(lastRowOfLastColIdx);
if (rowL != null){ testCell = rowL.getCell(lastColIdx);}
else testCell = null;
}
firstDataRow = lastRowOfLastColIdx;
firstColIdx = lastColIdx - headers.length;
if (noCountColumn == true) firstColIdx = firstColIdx + 1;
}

// Change the first column and first data row index to write data to, depending on whether an import cell is specified.
if (importCell != null) {
String[] inputCellParts = new String[3];
CellReference cellRef = new CellReference(importCell);
inputCellParts = cellRef.getCellRefParts();
firstDataRow = ((int) Integer.valueOf(inputCellParts[1]))-1;
firstColIdx = CellReference.convertColStringToIndex(inputCellParts[2]);
}

// Write dataset label to the first row in the sheet.
row = sheet.getRow(DATASET_LABEL_ROW);
if (row == null) row = sheet.createRow(DATASET_LABEL_ROW);
Expand All @@ -157,27 +240,14 @@ public void run(String arg) {
datasetLabelCell.setCellValue(dataSetLabel);
datasetLabelCell.setCellStyle(boldStyle);

// Write the column header cells.
row = sheet.getRow(COLUMN_HEADER_ROW);
if (row == null) row = sheet.createRow(COLUMN_HEADER_ROW);
for (int headerIdx = 0; headerIdx < (headers.length + idxAdj); headerIdx++) {
int cellCol = firstColIdx + headerIdx;
Cell colHeader = row.getCell(cellCol);
if (colHeader == null) colHeader = row.createCell(cellCol);
// Make sure we write the "Count" column header to the first column, if we want it.
if (cellCol == firstColIdx && !noCountColumn) colHeader.setCellValue("Count");
else colHeader.setCellValue(headers[headerIdx - idxAdj]);
colHeader.setCellStyle(boldStyle);
}

// Write the data (and count number, if necessary) to the sheet. All row/col numbers are 0-based indices.
// We loop over the actual 2D results array here, and figure out the cell row/col based on that.
row = sheet.getRow(FIRST_DATA_ROW);
for (int resultRow = 0; resultRow < results.length; resultRow++) {
// Figure out the cell row index, then get (or create) a row.
int cellRow = FIRST_DATA_ROW + resultRow;
int cellRow = firstDataRow + resultRow;
row = sheet.getRow(cellRow);
if (row == null) row = sheet.createRow(cellRow);

for (int resultCol = 0; resultCol < (results[resultRow].length + idxAdj); resultCol++) {
// Figure out the cell column index, then get (or create) a cell.
int cellCol = firstColIdx + resultCol;
Expand All @@ -186,15 +256,26 @@ public void run(String arg) {

// If this is the first cell column, and we want to write the row count, write that (1-based).
if (cellCol == firstColIdx && !noCountColumn) cell.setCellValue(resultRow + 1);
else cell.setCellValue(results[resultRow][resultCol - idxAdj]);
else {
//Check result datatype and format the cell appropriately before writing
//Not a perfect checking method, but will work most of the time without too much overhead
if (results[resultRow][resultCol - idxAdj].matches(".*[A-Za-z].*") == true || results[resultRow][resultCol - idxAdj] == " "){
cell.setCellValue(results[resultRow][resultCol - idxAdj]);
} else {
cell.setCellType(CellType.NUMERIC);
cell.setCellValue(Double.parseDouble(results[resultRow][resultCol - idxAdj]));
}
}
}
IJ.showProgress(resultRow, results.length + ((int)Math.rint(results.length/100)) );
}

// Write the output to a file.
if (fileHandlingMode == FileHandlingMode.OPEN_CLOSE) holderToUse.writeOutAndCloseWorkbook();
} catch (IOException e) {
IJ.handleException(e);
}
IJ.showProgress(1);
}

/**
Expand Down Expand Up @@ -256,6 +337,13 @@ private void parseOptions() {
ImagePlus currImage = WindowManager.getCurrentImage();
if (currImage != null) dataSetLabel = currImage.getTitle();
}

// Figure out if we want to place new results data into existing columns
// Stacking data instead of placing it adjacent to existing data in the designated spreadsheet
stackResults = optionsStr.contains("stack_results");

//Figure out if we want to import results data to a specific cell in the spreadsheet
importCell = Macro.getValue(optionsStr, "cell_ref", null);
}

private static class ExcelHolder {
Expand Down