protected override void ReadHeader(TileLoadInfo info)
{
info.OriginalPixelsPerMicron = 1.0;
info.OverLapPercentageX = 0.0;
info.OverLapPercentageY = 0.0;
this.arranger = new ImageCollectionArrangerForm();
TextStringDialog nameDialog = new TextStringDialog();
nameDialog.Text = "Mosaic Name";
nameDialog.Description = "Please enter a name for this Mosaic.";
nameDialog.ShowDialog();
this.dataSetName = nameDialog.TextString;
info.Prefix = this.dataSetName;
if (String.IsNullOrEmpty(this.dataSetName))
{
MessageBox.Show("Invalid Dataset name", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
Tile.IsCompositeRGB = false;
Tile.ThumbnailHeight = 0; // reset this so image aspect is correct
//this.imageCollectionThreadController = new ThreadController(this.arranger);
try
{
DisplayThumbnails();
}
catch (Exception e)
{
throw;
}
this.arranger.ShowDialog();
List <DesignerItem> items = this.arranger.GetItemPositionsSortedFromMostTopLeft();
float x, y, top, left;
Point position;
FreeImageAlgorithmsWPFImage wpfImage;
wpfImage = items[0].Content as FreeImageAlgorithmsWPFImage;
if (wpfImage == null)
{
throw new MosaicReaderException("UIElement is not a FreeImageAlgorithmsWPFImage type");
}
// Initialise left and top
left = (float)DesignerCanvas.GetLeft(items[0]);
top = (float)DesignerCanvas.GetTop(items[0]);
foreach (DesignerItem item in items)
{
wpfImage = item.Content as FreeImageAlgorithmsWPFImage;
if (wpfImage == null)
{
throw new MosaicReaderException("UIElement is not a FreeImageAlgorithmsWPFImage type");
}
// Get position of item relative to the most top left
x = (float)DesignerCanvas.GetLeft(item);
y = (float)DesignerCanvas.GetTop(item);
if (x < left)
{
left = x;
}
if (y < top)
{
top = y;
}
}
// We now have the most top left position.
foreach (DesignerItem item in items)
{
wpfImage = item.Content as FreeImageAlgorithmsWPFImage;
if (wpfImage == null)
{
throw new MosaicReaderException("UIElement is not a FreeImageAlgorithmsWPFImage type");
}
// Get position of item relative to the most top left
x = (float)DesignerCanvas.GetLeft(item) - left;
y = (float)DesignerCanvas.GetTop(item) - top;
position = new Point((int)x, (int)y);
Tile tile = new Tile(wpfImage.FilePath, position, wpfImage.Fib.Width, wpfImage.Fib.Height);
x = (int)(x / tile.ThumbnailToFullWidthScaleFactor);
y = (int)(y / tile.ThumbnailToFullHeightScaleFactor);
position = new Point((int)x, (int)y);
tile.OriginalPosition = position;
tile.ColorDepth = wpfImage.Fib.ColorDepth;
tile.FreeImageType = wpfImage.Fib.ImageType;
info.Items.Add(tile);
}
}
protected override void ReadHeader(TileLoadInfo info)
{
// TODO check all seqs have the same format
int count = 0;
List <TilePosition> tilePositions = new List <TilePosition>();
string prefix = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "file format", "");
string prefix2 = "", prefix3 = ""; // may not have 3 files, but should have 2
if (this.FilePaths.Length > 1)
{
prefix2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "file format", "");
Tile.nCompositeImages = 2;
}
if (this.FilePaths.Length > 2)
{
prefix3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "file format", "");
Tile.nCompositeImages = 3;
}
string iniValue, iniValue2, iniValue3;
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "roi left", "0.0");
double roiLeft = Convert.ToDouble(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "roi top", "0.0");
double roiTop = Convert.ToDouble(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Roi Height", "0.0");
double roiHeight = Convert.ToDouble(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Horizontal Overlap", "0.0");
iniValue2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Horizontal Overlap", "0.0");
if (iniValue != iniValue2)
{
throw new MosaicReaderException("Seq files have different Horizontal Overlap.");
}
if (Tile.nCompositeImages == 3)
{
iniValue3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Horizontal Overlap", "0.0");
if (iniValue != iniValue3)
{
throw new MosaicReaderException("Seq files have different Horizontal Overlap.");
}
}
// This is overlap in %
decimal overlapX = Convert.ToDecimal(iniValue);
info.OverLapPercentageX = (double)overlapX;
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Vertical Overlap", "0.0");
iniValue2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Vertical Overlap", "0.0");
if (iniValue != iniValue2)
{
throw new MosaicReaderException("Seq files have different Vertical Overlap.");
}
if (Tile.nCompositeImages == 3)
{
iniValue3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Vertical Overlap", "0.0");
if (iniValue != iniValue3)
{
throw new MosaicReaderException("Seq files have different Vertical Overlap.");
}
}
// This is overlap in %
decimal overlapY = Convert.ToDecimal(iniValue);
info.OverLapPercentageY = (double)overlapY;
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Horizontal Frames", "0.0");
info.WidthInTiles = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Vertical Frames", "0.0");
info.HeightInTiles = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Max Intensity", "0.0");
info.TotalMinIntensity = 0;
info.TotalMaxIntensity = Convert.ToDouble(iniValue, CultureInfo.InvariantCulture);
info.ScaleMinIntensity = info.TotalMinIntensity;
info.ScaleMaxIntensity = info.TotalMaxIntensity;
/* Tile.TotalMaxIntensity[0] = info.TotalMaxIntensity;
* iniValue = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Max Intensity", "0.0");
* Tile.TotalMaxIntensity[1] = Convert.ToDouble(iniValue, CultureInfo.InvariantCulture);
* if (Tile.nCompositeImages == 3)
* {
* iniValue = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Max Intensity", "0.0");
* Tile.TotalMaxIntensity[2] = Convert.ToDouble(iniValue, CultureInfo.InvariantCulture);
* }
*/
string extension = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Extension", ".ics");
string extension2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Extension", ".ics");
if (extension != extension2)
{
throw new MosaicReaderException("Seq files have different File types.");
}
if (Tile.nCompositeImages == 3)
{
string extension3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Extension", ".ics");
if (extension != extension3)
{
throw new MosaicReaderException("Seq files have different File types.");
}
}
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Tile Width", "0");
iniValue2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Tile Width", "0.0");
if (iniValue != iniValue2)
{
throw new MosaicReaderException("Seq files have different Tile Width.");
}
if (Tile.nCompositeImages == 3)
{
iniValue3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Tile Width", "0.0");
if (iniValue != iniValue3)
{
throw new MosaicReaderException("Seq files have different Tile Width.");
}
}
int tileWidth = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Tile Height", "0");
iniValue2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Tile Height", "0.0");
if (iniValue != iniValue2)
{
throw new MosaicReaderException("Seq files have different Tile Height.");
}
if (Tile.nCompositeImages == 3)
{
iniValue3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Tile Height", "0.0");
if (iniValue != iniValue3)
{
throw new MosaicReaderException("Seq files have different Tile Height.");
}
}
int tileHeight = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Tile Bits Per Pixel", "0");
iniValue2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Tile Bits Per Pixel", "0.0");
if (iniValue != iniValue2)
{
throw new MosaicReaderException("Seq files have different Tile Bits Per Pixel.");
}
if (Tile.nCompositeImages == 3)
{
iniValue3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Tile Bits Per Pixel", "0.0");
if (iniValue != iniValue3)
{
throw new MosaicReaderException("Seq files have different Tile Bits Per Pixel.");
}
}
info.ColorDepth = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Tile Image Type", "0");
iniValue2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Tile Image Type", "0.0");
if (iniValue != iniValue2)
{
throw new MosaicReaderException("Seq files have different Tile Image Type.");
}
if (Tile.nCompositeImages == 3)
{
iniValue3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Tile Image Type", "0.0");
if (iniValue != iniValue3)
{
throw new MosaicReaderException("Seq files have different Tile Image Type.");
}
}
int tileImageType = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Pixels Per Micron", "1.0");
iniValue2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Pixels Per Micron", "0.0");
if (iniValue != iniValue2)
{
throw new MosaicReaderException("Seq files have different Pixels Per Micron.");
}
if (Tile.nCompositeImages == 3)
{
iniValue3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Pixels Per Micron", "0.0");
if (iniValue != iniValue3)
{
throw new MosaicReaderException("Seq files have different Pixels Per Micron.");
}
}
info.OriginalPixelsPerMicron = Convert.ToDouble(iniValue, CultureInfo.InvariantCulture);
// This file format provides a list of tiles and their position relative
// to the left, top of the first region of interest.
// these prefix's are needed below, but let's ask for the prefix for the composite mosaic
TextStringDialog nameDialog = new TextStringDialog();
nameDialog.Text = "Composite Mosaic Name";
nameDialog.Description = "Please enter a name for this composite Mosaic.";
nameDialog.TextString = prefix + "_" + prefix2 + "_" + prefix3;
// if (Tile.nCompositeImages==3)
// nameDialog.TextString.
nameDialog.ShowDialog();
this.dataSetName = nameDialog.TextString;
Tile.channelPrefix[0] = prefix;
Tile.channelPrefix[1] = prefix2;
Tile.channelPrefix[2] = prefix3;
info.Prefix = this.dataSetName;
DirectoryInfo dir = new DirectoryInfo(this.DirectoryPath);
FileInfo[] filesInDir = dir.GetFiles(prefix + "*" + extension);
count = info.WidthInTiles * info.HeightInTiles;
Tile[] validTiles = new Tile[count];
Tile.IsCompositeRGB = true;
info.IsCompositeRGB = Tile.IsCompositeRGB;
// Check whether all the filenames we have are valid
for (int i = 1; i <= count; i++)
{
string filename = BuildExpectedFilename(prefix, i, extension);
string fullpath = this.DirectoryPath + Path.DirectorySeparatorChar + filename;
validTiles[i - 1] = new Tile(fullpath, i, tileWidth, tileHeight);
}
int width = 0;
int height = 0;
int bpp = 24; // always 24 bit colour for this reader
FREE_IMAGE_TYPE type = FREE_IMAGE_TYPE.FIT_BITMAP;
int max_posible_intensity = 256;
{ // pick a tile from the middle of the stack to get some info, this is a single channel
Tile tile = validTiles[validTiles.Length / 2];
FreeImageAlgorithmsBitmap fib = Tile.LoadFreeImageBitmapFromFile(tile.FilePath); // use fn that loads fib directly from filename as tiles are not properly set up yet
width = fib.Width;
height = fib.Height;
// bpp = fib.ColorDepth;
// type = fib.ImageType;
max_posible_intensity = Utilities.guessFibMaxValue(fib);
fib.Dispose();
}
foreach (Tile tile in validTiles)
{
if (this.ThreadController.ThreadAborted)
{
return;
}
Point position = new Point();
int row, col;
row = ((tile.TileNumber - 1) / info.WidthInTiles) + 1;
if ((row % 2) > 0)
{
// Odd row reversed order
col = ((tile.TileNumber - 1) % info.WidthInTiles) + 1;
}
else
{
// Even row nornal order
col = info.WidthInTiles - ((tile.TileNumber - 1) % info.WidthInTiles);
}
decimal overlapXInpixels = (overlapX / 100.0M) * (decimal)tileWidth;
decimal overlapYInpixels = (overlapY / 100.0M) * (decimal)tileHeight;
position.X = (int)Math.Round(((decimal)width - overlapXInpixels) * ((decimal)col - 1.0M));
position.Y = (int)Math.Round(((decimal)height - overlapYInpixels) * ((decimal)row - 1.0M));
tile.OriginalPosition = position;
tile.Width = width;
tile.Height = height;
tile.ColorDepth = bpp;
tile.FreeImageType = type;
// multi seq specific stuff
string filename = BuildExpectedFilename(prefix2, tile.TileNumber, extension);
tile.setFileName(1, filename);
if (Tile.nCompositeImages == 3)
{
filename = BuildExpectedFilename(prefix3, tile.TileNumber, extension);
tile.setFileName(2, filename);
}
info.Items.Add(tile);
}
Tile.scaleMin[0] = 0.0;
Tile.scaleMax[0] = (double)max_posible_intensity;
Tile.scaleMin[1] = 0.0;
Tile.scaleMax[1] = (double)max_posible_intensity;
Tile.scaleMin[2] = 0.0;
Tile.scaleMax[2] = (double)max_posible_intensity;
Tile.channelShift[0] = new Point(0, 0);
Tile.channelShift[1] = new Point(0, 0);
Tile.channelShift[2] = new Point(0, 0);
// check all files
bool oneNotFound = false, atLeastOneFound = false;
foreach (Tile tile in validTiles)
{
if (System.IO.File.Exists(tile.FilePath))
{
if (System.IO.File.Exists(tile.getFilePath(1)))
{
if (Tile.nCompositeImages == 3)
{
if (System.IO.File.Exists(tile.getFilePath(2)))
{
atLeastOneFound = true;
}
else
{
oneNotFound = true;
}
}
else
{
atLeastOneFound = true;
}
}
else
{
oneNotFound = true;
}
}
else
{
oneNotFound = true;
}
}
if (!atLeastOneFound) // No images at all!
{
throw (new MosaicReaderException("No tiles have all channels, images missing."));
}
if (oneNotFound)
{
MessageBox.Show("At least 1 image is missing from the mosaic.", "Warning", MessageBoxButtons.OK, MessageBoxIcon.Warning);
}
}
protected override void ReadHeader(TileLoadInfo info)
{
// TODO check all seqs have the same format
int count = 0;
List<TilePosition> tilePositions = new List<TilePosition>();
string prefix = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "file format", "");
string prefix2 = "", prefix3 = ""; // may not have 3 files, but should have 2
if (this.FilePaths.Length > 1)
{
prefix2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "file format", "");
Tile.nCompositeImages = 2;
}
if (this.FilePaths.Length > 2)
{
prefix3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "file format", "");
Tile.nCompositeImages = 3;
}
string iniValue, iniValue2, iniValue3;
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "roi left", "0.0");
double roiLeft = Convert.ToDouble(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "roi top", "0.0");
double roiTop = Convert.ToDouble(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Roi Height", "0.0");
double roiHeight = Convert.ToDouble(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Horizontal Overlap", "0.0");
iniValue2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Horizontal Overlap", "0.0");
if (iniValue != iniValue2) throw new MosaicReaderException("Seq files have different Horizontal Overlap.");
if (Tile.nCompositeImages == 3)
{
iniValue3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Horizontal Overlap", "0.0");
if (iniValue != iniValue3) throw new MosaicReaderException("Seq files have different Horizontal Overlap.");
}
// This is overlap in %
decimal overlapX = Convert.ToDecimal(iniValue);
info.OverLapPercentageX = (double)overlapX;
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Vertical Overlap", "0.0");
iniValue2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Vertical Overlap", "0.0");
if (iniValue != iniValue2) throw new MosaicReaderException("Seq files have different Vertical Overlap.");
if (Tile.nCompositeImages == 3)
{
iniValue3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Vertical Overlap", "0.0");
if (iniValue != iniValue3) throw new MosaicReaderException("Seq files have different Vertical Overlap.");
}
// This is overlap in %
decimal overlapY = Convert.ToDecimal(iniValue);
info.OverLapPercentageY = (double)overlapY;
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Horizontal Frames", "0.0");
info.WidthInTiles = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Vertical Frames", "0.0");
info.HeightInTiles = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Max Intensity", "0.0");
info.TotalMinIntensity = 0;
info.TotalMaxIntensity = Convert.ToDouble(iniValue, CultureInfo.InvariantCulture);
info.ScaleMinIntensity = info.TotalMinIntensity;
info.ScaleMaxIntensity = info.TotalMaxIntensity;
/* Tile.TotalMaxIntensity[0] = info.TotalMaxIntensity;
iniValue = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Max Intensity", "0.0");
Tile.TotalMaxIntensity[1] = Convert.ToDouble(iniValue, CultureInfo.InvariantCulture);
if (Tile.nCompositeImages == 3)
{
iniValue = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Max Intensity", "0.0");
Tile.TotalMaxIntensity[2] = Convert.ToDouble(iniValue, CultureInfo.InvariantCulture);
}
*/
string extension = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Extension", ".ics");
string extension2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Extension", ".ics");
if (extension != extension2) throw new MosaicReaderException("Seq files have different File types.");
if (Tile.nCompositeImages == 3)
{
string extension3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Extension", ".ics");
if (extension != extension3) throw new MosaicReaderException("Seq files have different File types.");
}
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Tile Width", "0");
iniValue2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Tile Width", "0.0");
if (iniValue != iniValue2) throw new MosaicReaderException("Seq files have different Tile Width.");
if (Tile.nCompositeImages == 3)
{
iniValue3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Tile Width", "0.0");
if (iniValue != iniValue3) throw new MosaicReaderException("Seq files have different Tile Width.");
}
int tileWidth = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Tile Height", "0");
iniValue2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Tile Height", "0.0");
if (iniValue != iniValue2) throw new MosaicReaderException("Seq files have different Tile Height.");
if (Tile.nCompositeImages == 3)
{
iniValue3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Tile Height", "0.0");
if (iniValue != iniValue3) throw new MosaicReaderException("Seq files have different Tile Height.");
}
int tileHeight = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Tile Bits Per Pixel", "0");
iniValue2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Tile Bits Per Pixel", "0.0");
if (iniValue != iniValue2) throw new MosaicReaderException("Seq files have different Tile Bits Per Pixel.");
if (Tile.nCompositeImages == 3)
{
iniValue3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Tile Bits Per Pixel", "0.0");
if (iniValue != iniValue3) throw new MosaicReaderException("Seq files have different Tile Bits Per Pixel.");
}
info.ColorDepth = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Tile Image Type", "0");
iniValue2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Tile Image Type", "0.0");
if (iniValue != iniValue2) throw new MosaicReaderException("Seq files have different Tile Image Type.");
if (Tile.nCompositeImages == 3)
{
iniValue3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Tile Image Type", "0.0");
if (iniValue != iniValue3) throw new MosaicReaderException("Seq files have different Tile Image Type.");
}
int tileImageType = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Pixels Per Micron", "1.0");
iniValue2 = IniParser.IniFile.GetIniFileString(this.FilePaths[1], info_ini_name, "Pixels Per Micron", "0.0");
if (iniValue != iniValue2) throw new MosaicReaderException("Seq files have different Pixels Per Micron.");
if (Tile.nCompositeImages == 3)
{
iniValue3 = IniParser.IniFile.GetIniFileString(this.FilePaths[2], info_ini_name, "Pixels Per Micron", "0.0");
if (iniValue != iniValue3) throw new MosaicReaderException("Seq files have different Pixels Per Micron.");
}
info.OriginalPixelsPerMicron = Convert.ToDouble(iniValue, CultureInfo.InvariantCulture);
// This file format provides a list of tiles and their position relative
// to the left, top of the first region of interest.
// these prefix's are needed below, but let's ask for the prefix for the composite mosaic
TextStringDialog nameDialog = new TextStringDialog();
nameDialog.Text = "Composite Mosaic Name";
nameDialog.Description = "Please enter a name for this composite Mosaic.";
nameDialog.TextString = prefix + "_" + prefix2 + "_" + prefix3;
// if (Tile.nCompositeImages==3)
// nameDialog.TextString.
nameDialog.ShowDialog();
this.dataSetName = nameDialog.TextString;
Tile.channelPrefix[0] = prefix;
Tile.channelPrefix[1] = prefix2;
Tile.channelPrefix[2] = prefix3;
info.Prefix = this.dataSetName;
DirectoryInfo dir = new DirectoryInfo(this.DirectoryPath);
FileInfo[] filesInDir = dir.GetFiles(prefix + "*" + extension);
count = info.WidthInTiles * info.HeightInTiles;
Tile[] validTiles = new Tile[count];
Tile.IsCompositeRGB = true;
info.IsCompositeRGB = Tile.IsCompositeRGB;
// Check whether all the filenames we have are valid
for (int i = 1; i <= count; i++)
{
string filename = BuildExpectedFilename(prefix, i, extension);
string fullpath = this.DirectoryPath + Path.DirectorySeparatorChar + filename;
validTiles[i - 1] = new Tile(fullpath, i, tileWidth, tileHeight);
}
int width = 0;
int height = 0;
int bpp = 24; // always 24 bit colour for this reader
FREE_IMAGE_TYPE type = FREE_IMAGE_TYPE.FIT_BITMAP;
int max_posible_intensity = 256;
{ // pick a tile from the middle of the stack to get some info, this is a single channel
Tile tile = validTiles[validTiles.Length / 2];
FreeImageAlgorithmsBitmap fib = Tile.LoadFreeImageBitmapFromFile(tile.FilePath); // use fn that loads fib directly from filename as tiles are not properly set up yet
width = fib.Width;
height = fib.Height;
// bpp = fib.ColorDepth;
// type = fib.ImageType;
max_posible_intensity = Utilities.guessFibMaxValue(fib);
fib.Dispose();
}
foreach (Tile tile in validTiles)
{
if (this.ThreadController.ThreadAborted)
return;
Point position = new Point();
int row, col;
row = ((tile.TileNumber - 1) / info.WidthInTiles) + 1;
if ((row % 2) > 0)
{
// Odd row reversed order
col = ((tile.TileNumber - 1) % info.WidthInTiles) + 1;
}
else
{
// Even row nornal order
col = info.WidthInTiles - ((tile.TileNumber - 1) % info.WidthInTiles);
}
decimal overlapXInpixels = (overlapX / 100.0M) * (decimal)tileWidth;
decimal overlapYInpixels = (overlapY / 100.0M) * (decimal)tileHeight;
position.X = (int)Math.Round(((decimal)width - overlapXInpixels) * ((decimal)col - 1.0M));
position.Y = (int)Math.Round(((decimal)height - overlapYInpixels) * ((decimal)row - 1.0M));
tile.OriginalPosition = position;
tile.Width = width;
tile.Height = height;
tile.ColorDepth = bpp;
tile.FreeImageType = type;
// multi seq specific stuff
string filename = BuildExpectedFilename(prefix2, tile.TileNumber, extension);
tile.setFileName(1, filename);
if (Tile.nCompositeImages == 3)
{
filename = BuildExpectedFilename(prefix3, tile.TileNumber, extension);
tile.setFileName(2, filename);
}
info.Items.Add(tile);
}
Tile.scaleMin[0] = 0.0;
Tile.scaleMax[0] = (double)max_posible_intensity;
Tile.scaleMin[1] = 0.0;
Tile.scaleMax[1] = (double)max_posible_intensity;
Tile.scaleMin[2] = 0.0;
Tile.scaleMax[2] = (double)max_posible_intensity;
Tile.channelShift[0] = new Point(0, 0);
Tile.channelShift[1] = new Point(0, 0);
Tile.channelShift[2] = new Point(0, 0);
// check all files
bool oneNotFound = false, atLeastOneFound = false;
foreach (Tile tile in validTiles)
{
if (System.IO.File.Exists(tile.FilePath))
{
if (System.IO.File.Exists(tile.getFilePath(1)))
{
if (Tile.nCompositeImages == 3)
{
if (System.IO.File.Exists(tile.getFilePath(2)))
atLeastOneFound = true;
else
oneNotFound = true;
}
else
atLeastOneFound = true;
}
else
oneNotFound = true;
}
else
oneNotFound = true;
}
if (!atLeastOneFound) // No images at all!
throw (new MosaicReaderException("No tiles have all channels, images missing."));
if (oneNotFound)
MessageBox.Show("At least 1 image is missing from the mosaic.", "Warning", MessageBoxButtons.OK, MessageBoxIcon.Warning);
}
protected override void ReadHeader(TileLoadInfo info)
{
info.OriginalPixelsPerMicron = 1.0;
info.OverLapPercentageX = 0.0;
info.OverLapPercentageY = 0.0;
this.arranger = new ImageCollectionArrangerForm();
TextStringDialog nameDialog = new TextStringDialog();
nameDialog.Text = "Mosaic Name";
nameDialog.Description = "Please enter a name for this Mosaic.";
nameDialog.ShowDialog();
this.dataSetName = nameDialog.TextString;
info.Prefix = this.dataSetName;
if (String.IsNullOrEmpty(this.dataSetName))
{
MessageBox.Show("Invalid Dataset name", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
Tile.IsCompositeRGB = false;
Tile.ThumbnailHeight = 0; // reset this so image aspect is correct
//this.imageCollectionThreadController = new ThreadController(this.arranger);
try
{
DisplayThumbnails();
}
catch (Exception e)
{
throw;
}
this.arranger.ShowDialog();
List<DesignerItem> items = this.arranger.GetItemPositionsSortedFromMostTopLeft();
float x, y, top, left;
Point position;
FreeImageAlgorithmsWPFImage wpfImage;
wpfImage = items[0].Content as FreeImageAlgorithmsWPFImage;
if (wpfImage == null)
{
throw new MosaicReaderException("UIElement is not a FreeImageAlgorithmsWPFImage type");
}
// Initialise left and top
left = (float)DesignerCanvas.GetLeft(items[0]);
top = (float)DesignerCanvas.GetTop(items[0]);
foreach (DesignerItem item in items)
{
wpfImage = item.Content as FreeImageAlgorithmsWPFImage;
if (wpfImage == null)
{
throw new MosaicReaderException("UIElement is not a FreeImageAlgorithmsWPFImage type");
}
// Get position of item relative to the most top left
x = (float)DesignerCanvas.GetLeft(item);
y = (float)DesignerCanvas.GetTop(item);
if (x < left)
left = x;
if (y < top)
top = y;
}
// We now have the most top left position.
foreach (DesignerItem item in items)
{
wpfImage = item.Content as FreeImageAlgorithmsWPFImage;
if(wpfImage == null)
{
throw new MosaicReaderException("UIElement is not a FreeImageAlgorithmsWPFImage type");
}
// Get position of item relative to the most top left
x = (float)DesignerCanvas.GetLeft(item) - left;
y = (float)DesignerCanvas.GetTop(item) - top;
position = new Point((int)x, (int)y);
Tile tile = new Tile(wpfImage.FilePath, position, wpfImage.Fib.Width, wpfImage.Fib.Height);
x = (int)(x / tile.ThumbnailToFullWidthScaleFactor);
y = (int)(y / tile.ThumbnailToFullHeightScaleFactor);
position = new Point((int)x, (int)y);
tile.OriginalPosition = position;
tile.ColorDepth = wpfImage.Fib.ColorDepth;
tile.FreeImageType = wpfImage.Fib.ImageType;
info.Items.Add(tile);
}
}