private bool ReadMetaData(TileLoadInfo info, string filepath)
{
if (!File.Exists(filepath))
{
return(false);
}
using (StreamReader file = System.IO.File.OpenText(filepath))
{
// Read file
while (!file.EndOfStream)
{
String line = file.ReadLine();
// Ignore empty lines
if (line.Length > 0)
{
string[] lineData = line.Split('\t');
info.AddMetaData(lineData[0], lineData[1]);
}
}
// Remove any silly values - Why do we export these from the scope ?
info.MetaData.Remove("stage pos");
info.MetaData.Remove("stage positionx");
info.MetaData.Remove("stage positiony");
info.MetaData.Remove("stage positionz");
}
return(true);
}
/*
public override void SetPrefix(TileLoadInfo info)
{
this.s = new ZipInputStream(File.OpenRead(this.FilePath));
this.sr = new StreamReader(s);
this.s.GetNextEntry(); // Get the first entry ie the info file.
string text = sr.ReadToEnd();
this.tileData = Regex.Split(text, "\r\n");
string[] line = this.tileData[0].Split('\u0000');
// Get the prefix of the tiles
info.Prefix = this.tileData[1].Split('\u0000')[0];
this.s.Close();
this.sr.Close();
}
*/
protected override void ReadHeader(TileLoadInfo info)
{
try
{
this.s = new ZipInputStream(File.OpenRead(this.FilePath));
this.sr = new StreamReader(s);
this.s.GetNextEntry(); // Get the first entry ie the info file.
string text = sr.ReadToEnd();
double version = 1.0;
this.tileData = Regex.Split(text, "\r\n");
string[] line = this.tileData[0].Split('\u0000');
int j = 0; // version number at start
version = Convert.ToDouble(line[j]); j++;
info.WidthInTiles = Convert.ToInt32(line[j]); j++;
info.HeightInTiles = Convert.ToInt32(line[j]); j++;
info.TotalWidth = Convert.ToInt32(line[j]); j++;
info.TotalHeight = Convert.ToInt32(line[j]); j++;
info.ColorDepth = Convert.ToInt32(line[j]); j++;
info.OriginalPixelsPerMicron = Convert.ToDouble(line[j]); j++;
info.OverLapPercentageX = Convert.ToDouble(line[j]); j++;
info.OverLapPercentageY = Convert.ToDouble(line[j]); j++;
double dummyOverlap = Convert.ToDouble(line[j]); j++;
info.TotalMinIntensity = Convert.ToDouble(line[j]); j++;
info.TotalMaxIntensity = Convert.ToDouble(line[j]); j++;
info.ScaleMinIntensity = info.TotalMinIntensity;
info.ScaleMaxIntensity = info.TotalMaxIntensity;
info.FreeImageType = (FREE_IMAGE_TYPE)Convert.ToInt32(line[j]); j++;
this.numberOfTiles = Convert.ToInt32(line[j]); j++;
this.thumbnailWidth = Convert.ToInt32(line[j]); j++;
this.thumbnailHeight = Convert.ToInt32(line[j]); j++;
info.IsCorrelated = Convert.ToBoolean(line[j]); j++;
info.Prefix = this.tileData[1].Split('\u0000')[0];
string filepath, filename, filename2="", filename3="";
int i = 1;
// Read the thumbnails
while (i <= this.numberOfTiles)
{
if (this.ThreadController.ThreadAborted)
return;
line = this.tileData[i + 1].Split('\u0000');
j = 0;
filename = line[j].ToString(); j++;
if (version >= 1.5) // composite images
{
filename2 = line[j].ToString(); j++;
filename3 = line[j].ToString(); j++;
}
filepath = this.DirectoryPath + Path.DirectorySeparatorChar + filename;
int x = Convert.ToInt32(line[j]); j++;
int y = Convert.ToInt32(line[j]); j++;
int width = Convert.ToInt32(line[j]); j++;
int height = Convert.ToInt32(line[j]); j++;
int bpp = Convert.ToInt32(line[j]); j++;
int minIntensity = Convert.ToInt32(line[j]); j++;
int maxIntensity = Convert.ToInt32(line[j]); j++;
int type = Convert.ToInt32(line[j]); j++;
bool isDummy = Convert.ToBoolean(line[j]); j++;
int correlatedx = Convert.ToInt32(line[j]); j++;
int correlatedy = Convert.ToInt32(line[j]); j++;
bool isCorrelated = Convert.ToBoolean(line[j]); j++;
Point position = new Point(x, y);
Point correlatedPosition = new Point(correlatedx, correlatedy);
Tile tile = new Tile(filepath, position, width, height);
tile.ColorDepth = bpp;
tile.FreeImageType = (FREE_IMAGE_TYPE)type;
tile.MinIntensity = minIntensity;
tile.MaxIntensity = maxIntensity;
tile.IsDummy = isDummy;
tile.AdjustedPosition = correlatedPosition;
tile.IsAdjusted = isCorrelated;
if (version >= 1.5) // composite images
{
tile.setFileName(1, filename2);
tile.setFileName(2, filename3);
}
info.Items.Add(tile);
i++;
}
if (version >= 1.5) // composite images
{
line = this.tileData[i + 1].Split('\u0000'); i++;
j = 0;
Tile.IsCompositeRGB = Convert.ToBoolean(line[j]); j++;
info.IsCompositeRGB = Tile.IsCompositeRGB;
Tile.nCompositeImages = Convert.ToInt32(line[j]); j++;
Tile.channel[0] = (FREE_IMAGE_COLOR_CHANNEL)Convert.ToInt32(line[j]); j++;
Tile.channel[1] = (FREE_IMAGE_COLOR_CHANNEL)Convert.ToInt32(line[j]); j++;
Tile.channel[2] = (FREE_IMAGE_COLOR_CHANNEL)Convert.ToInt32(line[j]); j++;
Tile.scaleMin[0] = Convert.ToDouble(line[j]); j++;
Tile.scaleMin[1] = Convert.ToDouble(line[j]); j++;
Tile.scaleMin[2] = Convert.ToDouble(line[j]); j++;
Tile.scaleMax[0] = Convert.ToDouble(line[j]); j++;
Tile.scaleMax[1] = Convert.ToDouble(line[j]); j++;
Tile.scaleMax[2] = Convert.ToDouble(line[j]); j++;
if (version >= 1.6) // composite rgb channel shifts
{
Tile.channelShift[0].X = Convert.ToInt32(line[j]); j++;
Tile.channelShift[0].Y = Convert.ToInt32(line[j]); j++;
Tile.channelShift[1].X = Convert.ToInt32(line[j]); j++;
Tile.channelShift[1].Y = Convert.ToInt32(line[j]); j++;
Tile.channelShift[2].X = Convert.ToInt32(line[j]); j++;
Tile.channelShift[2].Y = Convert.ToInt32(line[j]); j++;
}
Tile.channelPrefix[0] = this.tileData[i + 1].Split('\u0000')[0]; i++;
Tile.channelPrefix[1] = this.tileData[i + 1].Split('\u0000')[0]; i++;
Tile.channelPrefix[2] = this.tileData[i + 1].Split('\u0000')[0]; i++;
}
else
{
Tile.IsCompositeRGB = false;
info.IsCompositeRGB = false;
}
this.s.Close();
this.sr.Close();
}
catch (System.FormatException)
{
// probably an old mos file
// just continue to 'finally' section
MessageBox.Show("Old mos file imported.");
}
catch (Exception e)
{
throw new MosaicCacheReaderException("Failed to read cache file format: " + e.Message);
}
finally
{
this.s.Close();
this.sr.Close();
}
}
internal override void ReadThumbnails(TileLoadInfo info)
{
this.ThreadController.ReportThreadStarted(this, "Loading files");
ZipEntry zipEntry;
int totalCount = 0;
int count = 0;
ThumbnailMapCollection mapCollection =
new ThumbnailMapCollection(this.thumbnailWidth, this.thumbnailHeight);
this.s.Close();
this.s = new ZipInputStream(File.OpenRead(this.FilePath));
totalCount = 0;
try
{
// First go through the zip file and get the image maps
while ((zipEntry = this.s.GetNextEntry()) != null)
{
if (zipEntry.Name.StartsWith("Thumbnail"))
{
if (this.ThreadController.ThreadAborted)
return;
count = 0;
ThumbnailMap map = new ThumbnailMap(this.thumbnailWidth, this.thumbnailHeight, this.s);
Tile tile = null;
for (int i = 0; i < map.MapSizeInTiles && totalCount < MosaicWindow.MosaicInfo.Items.Count; i++)
{
tile = MosaicWindow.MosaicInfo.Items[totalCount];
FreeImageAlgorithmsBitmap fib = map.GetImage(count);
tile.Thumbnail = fib;
if (tile.Thumbnail == null)
{
throw new Exception("Failed to retrive tumbnail from map");
}
this.ThreadController.ReportThreadPercentage(this, "Creating Thumbnails",
totalCount++, MosaicWindow.MosaicInfo.Items.Count);
count++;
}
map.Dispose();
}
}
}
catch (Exception e)
{
MessageBox.Show(e.Message);
FailedToReadFormat = true;
this.ThreadController.ReportThreadCompleted(this, "Loaded file", false);
return;
}
this.s.Close();
this.sr.Close();
info.FreeImageType = MosaicWindow.MosaicInfo.Items[0].FreeImageType;
info.ColorDepth = MosaicWindow.MosaicInfo.Items[0].ColorDepth;
this.ThreadController.ReportThreadCompleted(this, "Loaded file", false);
}
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);
}
internal void RegenerateThumbnails(TileLoadInfo info)
{ // this is never overidden by a TileReader
double min = Double.MaxValue, max = Double.MinValue;
double tmp_min = 0.0, tmp_max = 0.0;
int count = 0;
this.threadController.ReportThreadStarted(this, "Creating Thumbnails");
foreach (Tile tile in info.Items)
{
if (this.threadController.ThreadAborted)
{
return;
}
using (FreeImageAlgorithmsBitmap fib = tile.LoadFreeImageBitmap())
{
Tile.ResizeToThumbnail(fib);
if (info.TotalMaxIntensity == 0.0)
{
// We have to find the max intensity of all the images then linear scale later
fib.FindMinMaxIntensity(out tmp_min, out tmp_max);
if (tmp_min < min)
{
min = tmp_min;
}
if (tmp_max > max)
{
max = tmp_max;
}
info.TotalMinIntensity = min;
info.TotalMaxIntensity = max;
info.ScaleMinIntensity = min;
info.ScaleMaxIntensity = max;
}
lock (tile.ThumbnailLock)
{
tile.Thumbnail = new FreeImageAlgorithmsBitmap(fib);
if (tile.Thumbnail == null)
{
MessageBox.Show("Error creating thumbnail.");
}
if (fib.IsGreyScale)
{
tile.Thumbnail.LinearScaleToStandardType(info.ScaleMinIntensity, info.ScaleMaxIntensity);
tile.Thumbnail.SetGreyLevelPalette();
}
}
this.threadController.ReportThreadPercentage(this, "Creating Thumbnails", count++, info.Items.Count);
}
}
// Have to scale the bitmaps for Ros's formats
if (info.TotalMaxIntensity != 0.0)
{
info.FreeImageType = info.Items[0].FreeImageType;
info.ColorDepth = info.Items[0].ColorDepth;
}
else
{
info.ScaleMinIntensity = min;
info.ScaleMaxIntensity = max;
count = 0;
info.FreeImageType = info.Items[0].FreeImageType;
info.ColorDepth = info.Items[0].ColorDepth;
}
this.threadController.ReportThreadCompleted(this, "Loaded Thumbnails", false);
}
internal virtual void ReadThumbnails(TileLoadInfo info)
{ // this may be overridden by a TileReader
RegenerateThumbnails(info);
}
protected override void ReadHeader(TileLoadInfo info)
{
int count = 0;
string extension = null;
decimal OverLapMicrons = 0M;
info.Prefix = System.IO.Path.GetFileNameWithoutExtension(this.FilePath);
info.DirectoryPath = System.IO.Path.GetDirectoryName(this.FilePath);
// Create an instance of StreamReader to read from a file.
// The using statement also closes the StreamReader.
using (StreamReader sr = new StreamReader(this.FilePath))
{
String line;
string[] fields;
try
{
// Read extents but don't use
line = sr.ReadLine();
// Get the overlap in microns
line = sr.ReadLine();
OverLapMicrons = Convert.ToDecimal(line);
// Get the number of frames in each direction
line = sr.ReadLine();
fields = line.Split('\t');
info.WidthInTiles = Convert.ToInt32(fields[0], CultureInfo.InvariantCulture);
info.HeightInTiles = Convert.ToInt32(fields[1], CultureInfo.InvariantCulture);
// Get the microns per pixel factor
line = sr.ReadLine();
info.OriginalPixelsPerMicron = Convert.ToDouble(line, CultureInfo.InvariantCulture);
// Get the extension of the files
extension = sr.ReadLine();
}
catch (IOException e)
{
System.Windows.Forms.MessageBox.Show("Cannot parse file: " + e.Message);
}
}
DirectoryInfo dir = new DirectoryInfo(this.DirectoryPath);
FileInfo[] filesInDir = dir.GetFiles(info.Prefix + "*" + extension);
count = info.WidthInTiles * info.HeightInTiles;
Tile[] validTiles = new Tile[count];
Tile.IsCompositeRGB = false;
// Check whether all the filenames will have are valid
for (int i = 1; i <= count; i++)
{
string filename = BuildExpectedFilename(info.Prefix, i, extension);
string fullpath = this.DirectoryPath + System.IO.Path.DirectorySeparatorChar + filename;
validTiles[i - 1] = new Tile(fullpath, i, 0, 0);
}
int width = 0;
int height = 0;
int bpp = 8;
FREE_IMAGE_TYPE type = FREE_IMAGE_TYPE.FIT_BITMAP;
// Find the first tile that exists to get the sizes and color depth etc
// but check all
bool oneNotFound = false, atLeastOneFound = false;
foreach (Tile tile in validTiles)
{
if (System.IO.File.Exists(tile.FilePath))
{
if (!atLeastOneFound)
{
FreeImageAlgorithmsBitmap fib = tile.LoadFreeImageBitmap();
width = fib.Width;
height = fib.Height;
bpp = fib.ColorDepth;
type = fib.ImageType;
fib.Dispose();
// Set the overlap percentage
double widthInMicrions = width / info.OriginalPixelsPerMicron;
double heightInMicrions = height / info.OriginalPixelsPerMicron;
info.OverLapPercentageX =
(double)((double)OverLapMicrons / widthInMicrions) * 100.0;
info.OverLapPercentageY =
(double)((double)OverLapMicrons / heightInMicrions) * 100.0;
atLeastOneFound = true;
}
}
else
{
oneNotFound = true;
}
}
if (!atLeastOneFound) // No images at all!
{
throw (new MosaicReaderException("No images found."));
}
if (oneNotFound)
{
MessageBox.Show("At least 1 image is missing from the mosaic.", "Warning", MessageBoxButtons.OK, MessageBoxIcon.Warning);
}
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);
}
// The original seq spec only allowed for one overlap in microns (not X and Y)
decimal overlapXInpixels = ((decimal)info.OverLapPercentageX / 100.0M) * (decimal)width;
decimal overlapYInpixels = ((decimal)info.OverLapPercentageY / 100.0M) * (decimal)height;
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;
info.Items.Add(tile);
}
}
protected override void ReadHeader(TileLoadInfo info)
{
int count = 0;
decimal OverLapMicrons = 0M;
FileInfo[] filesInDir = null;
List<TilePosition> tilePositions = new List<TilePosition>();
// Create an instance of StreamReader to read from a file.
// The using statement also closes the StreamReader.
using (StreamReader sr = new StreamReader(this.FilePath))
{
String line;
string[] fields;
try
{
// Read extents but don't use
line = sr.ReadLine();
// Get the overlap
line = sr.ReadLine();
OverLapMicrons = Convert.ToDecimal(line);
// Get the number of frames in each direction
line = sr.ReadLine();
fields = line.Split('\t');
info.WidthInTiles = Convert.ToInt32(fields[0], CultureInfo.InvariantCulture);
info.HeightInTiles = Convert.ToInt32(fields[1], CultureInfo.InvariantCulture);
// Get the microns per pixel factor
line = sr.ReadLine();
info.OriginalPixelsPerMicron = Convert.ToDouble(line, CultureInfo.InvariantCulture);
// By definition Ros's TileLoadInfo files consist of correlated data.
info.IsCorrelated = true;
// Get the extension of the files
line = sr.ReadLine();
filesInDir = new FileInfo[info.NumberOfTiles];
count = 0;
while ((line = sr.ReadLine()) != null)
{
fields = line.Split('\t');
tilePositions.Add(new TilePosition(fields[0],
Convert.ToInt32(fields[1], CultureInfo.InvariantCulture),
Convert.ToInt32(fields[2], CultureInfo.InvariantCulture)));
filesInDir[count++] = new FileInfo(this.DirectoryPath
+ "\\" + fields[0]);
}
}
catch (IOException e)
{
System.Windows.Forms.MessageBox.Show("Cannot parse file: " + e.Message);
}
}
Tile.IsCompositeRGB = false;
count = 0;
int width = 0;
int height = 0;
int bpp = 8;
FREE_IMAGE_TYPE type = FREE_IMAGE_TYPE.FIT_BITMAP;
// Find the first tile that exists to get the sizes and color depth etc
// but check all
bool oneNotFound = false, atLeastOneFound = false;
foreach (FileInfo file in filesInDir)
{
if (System.IO.File.Exists(file.FullName))
{
if (!atLeastOneFound)
{
FreeImageAlgorithmsBitmap fib = Tile.LoadFreeImageBitmapFromFile(file.FullName);
width = fib.Width;
height = fib.Height;
bpp = fib.ColorDepth;
type = fib.ImageType;
fib.Dispose();
// Set the overlap percentage
double widthInMicrions = width / info.OriginalPixelsPerMicron;
double heightInMicrions = height / info.OriginalPixelsPerMicron;
info.OverLapPercentageX =
(double)((double)OverLapMicrons / widthInMicrions) * 100.0;
info.OverLapPercentageY =
(double)((double)OverLapMicrons / heightInMicrions) * 100.0;
atLeastOneFound = true;
}
}
else
oneNotFound = true;
}
if (!atLeastOneFound) // No images at all!
throw (new MosaicReaderException("No images found."));
if (oneNotFound)
MessageBox.Show("At least 1 image is missing from the mosaic.", "Warning", MessageBoxButtons.OK, MessageBoxIcon.Warning);
foreach (FileInfo file in filesInDir)
{
if (this.ThreadController.ThreadAborted)
return;
if (!this.AllowedExtensions.Contains(file.Extension))
continue;
Point position = new Point();
position.X = tilePositions[count].X;
position.Y = tilePositions[count].Y;
Tile tile = new Tile(file.FullName, position, width, height);
tile.Width = width;
tile.Height = height;
tile.ColorDepth = bpp;
tile.FreeImageType = (FREE_IMAGE_TYPE) type;
info.Items.Add(tile);
count++;
}
}
protected override void ReadHeader(TileLoadInfo info)
{
int count = 0;
List<TilePosition> tilePositions = new List<TilePosition>();
string prefix = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "file format", "");
info.Prefix = prefix;
string 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");
// 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");
// 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;
string extension = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Extension", ".ics");
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Tile Width", "0");
int tileWidth = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Tile Height", "0");
int tileHeight = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Tile Bits Per Pixel", "0");
info.ColorDepth = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Tile Image Type", "0");
int tileImageType = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Pixels Per Micron", "1.0");
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.
DirectoryInfo dir = new DirectoryInfo(this.DirectoryPath);
FileInfo[] filesInDir = dir.GetFiles(prefix + "*" + extension);
count = info.WidthInTiles * info.HeightInTiles;
Tile[] validTiles = new Tile[count];
Tile.IsCompositeRGB = false;
// Check whether all the filenames will 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 = 8;
FREE_IMAGE_TYPE type = FREE_IMAGE_TYPE.FIT_BITMAP;
// Find the first tile that exists to get the sizes and color depth etc
// but check all
bool oneNotFound = false, atLeastOneFound = false;
foreach (Tile tile in validTiles)
{
if (System.IO.File.Exists(tile.FilePath))
{
if (!atLeastOneFound)
{
FreeImageAlgorithmsBitmap fib = tile.LoadFreeImageBitmap();
width = fib.Width;
height = fib.Height;
bpp = fib.ColorDepth;
type = fib.ImageType;
fib.Dispose();
atLeastOneFound = true;
}
}
else
oneNotFound = true;
}
if (!atLeastOneFound) // No images at all!
throw (new MosaicReaderException("No images found. Expecting prefix " + prefix + " as in seq file."));
if (oneNotFound)
MessageBox.Show("At least 1 image is missing from the mosaic.", "Warning", MessageBoxButtons.OK, MessageBoxIcon.Warning);
foreach (Tile tile in validTiles)
{
if (this.ThreadController.ThreadAborted)
return;
Point position = new Point();
int row, col;
// fileWithoutExtension = System.IO.Path.GetFileNameWithoutExtension(filepath);
// Ignore files in the directory that have shorter names than we expect.
// if (fileWithoutExtension.Length < mosaicInfo.Fileinfo.Prefix.Length)
// continue;
// fileWithoutPrefix = fileWithoutExtension.Substring(prefix.Length);
// fileNumber = Version2SequenceFileReader.ParseIntStringWithZeros(fileWithoutPrefix);
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;
info.Items.Add(tile);
}
}
/*
* public override void SetPrefix(TileLoadInfo info)
* {
* this.s = new ZipInputStream(File.OpenRead(this.FilePath));
* this.sr = new StreamReader(s);
* this.s.GetNextEntry(); // Get the first entry ie the info file.
*
* string text = sr.ReadToEnd();
*
* this.tileData = Regex.Split(text, "\r\n");
* string[] line = this.tileData[0].Split('\u0000');
*
* // Get the prefix of the tiles
* info.Prefix = this.tileData[1].Split('\u0000')[0];
*
* this.s.Close();
* this.sr.Close();
* }
*/
protected override void ReadHeader(TileLoadInfo info)
{
try
{
this.s = new ZipInputStream(File.OpenRead(this.FilePath));
this.sr = new StreamReader(s);
this.s.GetNextEntry(); // Get the first entry ie the info file.
string text = sr.ReadToEnd();
double version = 1.0;
this.tileData = Regex.Split(text, "\r\n");
string[] line = this.tileData[0].Split('\u0000');
int j = 0; // version number at start
version = Convert.ToDouble(line[j]); j++;
info.WidthInTiles = Convert.ToInt32(line[j]); j++;
info.HeightInTiles = Convert.ToInt32(line[j]); j++;
info.TotalWidth = Convert.ToInt32(line[j]); j++;
info.TotalHeight = Convert.ToInt32(line[j]); j++;
info.ColorDepth = Convert.ToInt32(line[j]); j++;
info.OriginalPixelsPerMicron = Convert.ToDouble(line[j]); j++;
info.OverLapPercentageX = Convert.ToDouble(line[j]); j++;
info.OverLapPercentageY = Convert.ToDouble(line[j]); j++;
double dummyOverlap = Convert.ToDouble(line[j]); j++;
info.TotalMinIntensity = Convert.ToDouble(line[j]); j++;
info.TotalMaxIntensity = Convert.ToDouble(line[j]); j++;
info.ScaleMinIntensity = info.TotalMinIntensity;
info.ScaleMaxIntensity = info.TotalMaxIntensity;
info.FreeImageType = (FREE_IMAGE_TYPE)Convert.ToInt32(line[j]); j++;
this.numberOfTiles = Convert.ToInt32(line[j]); j++;
this.thumbnailWidth = Convert.ToInt32(line[j]); j++;
this.thumbnailHeight = Convert.ToInt32(line[j]); j++;
info.IsCorrelated = Convert.ToBoolean(line[j]); j++;
info.Prefix = this.tileData[1].Split('\u0000')[0];
string filepath, filename, filename2 = "", filename3 = "";
int i = 1;
// Read the thumbnails
while (i <= this.numberOfTiles)
{
if (this.ThreadController.ThreadAborted)
{
return;
}
line = this.tileData[i + 1].Split('\u0000');
j = 0;
filename = line[j].ToString(); j++;
if (version >= 1.5) // composite images
{
filename2 = line[j].ToString(); j++;
filename3 = line[j].ToString(); j++;
}
filepath = this.DirectoryPath + Path.DirectorySeparatorChar + filename;
int x = Convert.ToInt32(line[j]); j++;
int y = Convert.ToInt32(line[j]); j++;
int width = Convert.ToInt32(line[j]); j++;
int height = Convert.ToInt32(line[j]); j++;
int bpp = Convert.ToInt32(line[j]); j++;
int minIntensity = Convert.ToInt32(line[j]); j++;
int maxIntensity = Convert.ToInt32(line[j]); j++;
int type = Convert.ToInt32(line[j]); j++;
bool isDummy = Convert.ToBoolean(line[j]); j++;
int correlatedx = Convert.ToInt32(line[j]); j++;
int correlatedy = Convert.ToInt32(line[j]); j++;
bool isCorrelated = Convert.ToBoolean(line[j]); j++;
Point position = new Point(x, y);
Point correlatedPosition = new Point(correlatedx, correlatedy);
Tile tile = new Tile(filepath, position, width, height);
tile.ColorDepth = bpp;
tile.FreeImageType = (FREE_IMAGE_TYPE)type;
tile.MinIntensity = minIntensity;
tile.MaxIntensity = maxIntensity;
tile.IsDummy = isDummy;
tile.AdjustedPosition = correlatedPosition;
tile.IsAdjusted = isCorrelated;
if (version >= 1.5) // composite images
{
tile.setFileName(1, filename2);
tile.setFileName(2, filename3);
}
info.Items.Add(tile);
i++;
}
if (version >= 1.5) // composite images
{
line = this.tileData[i + 1].Split('\u0000'); i++;
j = 0;
Tile.IsCompositeRGB = Convert.ToBoolean(line[j]); j++;
info.IsCompositeRGB = Tile.IsCompositeRGB;
Tile.nCompositeImages = Convert.ToInt32(line[j]); j++;
Tile.channel[0] = (FREE_IMAGE_COLOR_CHANNEL)Convert.ToInt32(line[j]); j++;
Tile.channel[1] = (FREE_IMAGE_COLOR_CHANNEL)Convert.ToInt32(line[j]); j++;
Tile.channel[2] = (FREE_IMAGE_COLOR_CHANNEL)Convert.ToInt32(line[j]); j++;
Tile.scaleMin[0] = Convert.ToDouble(line[j]); j++;
Tile.scaleMin[1] = Convert.ToDouble(line[j]); j++;
Tile.scaleMin[2] = Convert.ToDouble(line[j]); j++;
Tile.scaleMax[0] = Convert.ToDouble(line[j]); j++;
Tile.scaleMax[1] = Convert.ToDouble(line[j]); j++;
Tile.scaleMax[2] = Convert.ToDouble(line[j]); j++;
if (version >= 1.6) // composite rgb channel shifts
{
Tile.channelShift[0].X = Convert.ToInt32(line[j]); j++;
Tile.channelShift[0].Y = Convert.ToInt32(line[j]); j++;
Tile.channelShift[1].X = Convert.ToInt32(line[j]); j++;
Tile.channelShift[1].Y = Convert.ToInt32(line[j]); j++;
Tile.channelShift[2].X = Convert.ToInt32(line[j]); j++;
Tile.channelShift[2].Y = Convert.ToInt32(line[j]); j++;
}
Tile.channelPrefix[0] = this.tileData[i + 1].Split('\u0000')[0]; i++;
Tile.channelPrefix[1] = this.tileData[i + 1].Split('\u0000')[0]; i++;
Tile.channelPrefix[2] = this.tileData[i + 1].Split('\u0000')[0]; i++;
}
else
{
Tile.IsCompositeRGB = false;
info.IsCompositeRGB = false;
}
this.s.Close();
this.sr.Close();
}
catch (System.FormatException)
{
// probably an old mos file
// just continue to 'finally' section
MessageBox.Show("Old mos file imported.");
}
catch (Exception e)
{
throw new MosaicCacheReaderException("Failed to read cache file format: " + e.Message);
}
finally
{
this.s.Close();
this.sr.Close();
}
}
internal override void ReadThumbnails(TileLoadInfo info)
{
this.ThreadController.ReportThreadStarted(this, "Loading files");
ZipEntry zipEntry;
int totalCount = 0;
int count = 0;
ThumbnailMapCollection mapCollection =
new ThumbnailMapCollection(this.thumbnailWidth, this.thumbnailHeight);
this.s.Close();
this.s = new ZipInputStream(File.OpenRead(this.FilePath));
totalCount = 0;
try
{
// First go through the zip file and get the image maps
while ((zipEntry = this.s.GetNextEntry()) != null)
{
if (zipEntry.Name.StartsWith("Thumbnail"))
{
if (this.ThreadController.ThreadAborted)
{
return;
}
count = 0;
ThumbnailMap map = new ThumbnailMap(this.thumbnailWidth, this.thumbnailHeight, this.s);
Tile tile = null;
for (int i = 0; i < map.MapSizeInTiles && totalCount < MosaicWindow.MosaicInfo.Items.Count; i++)
{
tile = MosaicWindow.MosaicInfo.Items[totalCount];
FreeImageAlgorithmsBitmap fib = map.GetImage(count);
tile.Thumbnail = fib;
if (tile.Thumbnail == null)
{
throw new Exception("Failed to retrive tumbnail from map");
}
this.ThreadController.ReportThreadPercentage(this, "Creating Thumbnails",
totalCount++, MosaicWindow.MosaicInfo.Items.Count);
count++;
}
map.Dispose();
}
}
}
catch (Exception e)
{
MessageBox.Show(e.Message);
FailedToReadFormat = true;
this.ThreadController.ReportThreadCompleted(this, "Loaded file", false);
return;
}
this.s.Close();
this.sr.Close();
info.FreeImageType = MosaicWindow.MosaicInfo.Items[0].FreeImageType;
info.ColorDepth = MosaicWindow.MosaicInfo.Items[0].ColorDepth;
this.ThreadController.ReportThreadCompleted(this, "Loaded file", false);
}
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)
{
int count = 0;
string extension = null;
decimal OverLapMicrons=0M;
info.Prefix = System.IO.Path.GetFileNameWithoutExtension(this.FilePath);
info.DirectoryPath = System.IO.Path.GetDirectoryName(this.FilePath);
// Create an instance of StreamReader to read from a file.
// The using statement also closes the StreamReader.
using (StreamReader sr = new StreamReader(this.FilePath))
{
String line;
string[] fields;
try
{
// Read extents but don't use
line = sr.ReadLine();
// Get the overlap in microns
line = sr.ReadLine();
OverLapMicrons = Convert.ToDecimal(line);
// Get the number of frames in each direction
line = sr.ReadLine();
fields = line.Split('\t');
info.WidthInTiles = Convert.ToInt32(fields[0], CultureInfo.InvariantCulture);
info.HeightInTiles = Convert.ToInt32(fields[1], CultureInfo.InvariantCulture);
// Get the microns per pixel factor
line = sr.ReadLine();
info.OriginalPixelsPerMicron = Convert.ToDouble(line, CultureInfo.InvariantCulture);
// Get the extension of the files
extension = sr.ReadLine();
}
catch (IOException e)
{
System.Windows.Forms.MessageBox.Show("Cannot parse file: " + e.Message);
}
}
DirectoryInfo dir = new DirectoryInfo(this.DirectoryPath);
FileInfo[] filesInDir = dir.GetFiles(info.Prefix + "*" + extension);
count = info.WidthInTiles * info.HeightInTiles;
Tile[] validTiles = new Tile[count];
Tile.IsCompositeRGB = false;
// Check whether all the filenames will have are valid
for (int i = 1; i <= count; i++)
{
string filename = BuildExpectedFilename(info.Prefix, i, extension);
string fullpath = this.DirectoryPath + System.IO.Path.DirectorySeparatorChar + filename;
validTiles[i - 1] = new Tile(fullpath, i, 0, 0);
}
int width = 0;
int height = 0;
int bpp = 8;
FREE_IMAGE_TYPE type = FREE_IMAGE_TYPE.FIT_BITMAP;
// Find the first tile that exists to get the sizes and color depth etc
// but check all
bool oneNotFound = false, atLeastOneFound = false;
foreach (Tile tile in validTiles)
{
if (System.IO.File.Exists(tile.FilePath))
{
if (!atLeastOneFound)
{
FreeImageAlgorithmsBitmap fib = tile.LoadFreeImageBitmap();
width = fib.Width;
height = fib.Height;
bpp = fib.ColorDepth;
type = fib.ImageType;
fib.Dispose();
// Set the overlap percentage
double widthInMicrions = width / info.OriginalPixelsPerMicron;
double heightInMicrions = height / info.OriginalPixelsPerMicron;
info.OverLapPercentageX =
(double)((double)OverLapMicrons / widthInMicrions) * 100.0;
info.OverLapPercentageY =
(double)((double)OverLapMicrons / heightInMicrions) * 100.0;
atLeastOneFound = true;
}
}
else
oneNotFound = true;
}
if (!atLeastOneFound) // No images at all!
throw (new MosaicReaderException("No images found."));
if (oneNotFound)
MessageBox.Show("At least 1 image is missing from the mosaic.", "Warning", MessageBoxButtons.OK, MessageBoxIcon.Warning);
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);
}
// The original seq spec only allowed for one overlap in microns (not X and Y)
decimal overlapXInpixels = ((decimal)info.OverLapPercentageX / 100.0M) * (decimal)width;
decimal overlapYInpixels = ((decimal)info.OverLapPercentageY / 100.0M) * (decimal)height;
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;
info.Items.Add(tile);
}
}
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)
{
int count = 0;
List <TilePosition> tilePositions = new List <TilePosition>();
string prefix = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "file format", "");
info.Prefix = prefix;
string 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");
// 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");
// 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;
string extension = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Extension", ".ics");
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Tile Width", "0");
int tileWidth = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Tile Height", "0");
int tileHeight = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Tile Bits Per Pixel", "0");
info.ColorDepth = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Tile Image Type", "0");
int tileImageType = Convert.ToInt32(iniValue, CultureInfo.InvariantCulture);
iniValue = IniParser.IniFile.GetIniFileString(this.FilePath, info_ini_name, "Pixels Per Micron", "1.0");
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.
DirectoryInfo dir = new DirectoryInfo(this.DirectoryPath);
FileInfo[] filesInDir = dir.GetFiles(prefix + "*" + extension);
count = info.WidthInTiles * info.HeightInTiles;
Tile[] validTiles = new Tile[count];
Tile.IsCompositeRGB = false;
// Check whether all the filenames will 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 = 8;
FREE_IMAGE_TYPE type = FREE_IMAGE_TYPE.FIT_BITMAP;
// Find the first tile that exists to get the sizes and color depth etc
// but check all
bool oneNotFound = false, atLeastOneFound = false;
foreach (Tile tile in validTiles)
{
if (System.IO.File.Exists(tile.FilePath))
{
if (!atLeastOneFound)
{
FreeImageAlgorithmsBitmap fib = tile.LoadFreeImageBitmap();
width = fib.Width;
height = fib.Height;
bpp = fib.ColorDepth;
type = fib.ImageType;
fib.Dispose();
atLeastOneFound = true;
}
}
else
{
oneNotFound = true;
}
}
if (!atLeastOneFound) // No images at all!
{
throw (new MosaicReaderException("No images found. Expecting prefix " + prefix + " as in seq file."));
}
if (oneNotFound)
{
MessageBox.Show("At least 1 image is missing from the mosaic.", "Warning", MessageBoxButtons.OK, MessageBoxIcon.Warning);
}
foreach (Tile tile in validTiles)
{
if (this.ThreadController.ThreadAborted)
{
return;
}
Point position = new Point();
int row, col;
// fileWithoutExtension = System.IO.Path.GetFileNameWithoutExtension(filepath);
// Ignore files in the directory that have shorter names than we expect.
// if (fileWithoutExtension.Length < mosaicInfo.Fileinfo.Prefix.Length)
// continue;
// fileWithoutPrefix = fileWithoutExtension.Substring(prefix.Length);
// fileNumber = Version2SequenceFileReader.ParseIntStringWithZeros(fileWithoutPrefix);
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;
info.Items.Add(tile);
}
}
protected abstract void ReadHeader(TileLoadInfo info);
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)
{
int count = 0;
decimal OverLapMicrons = 0M;
FileInfo[] filesInDir = null;
List <TilePosition> tilePositions = new List <TilePosition>();
// Create an instance of StreamReader to read from a file.
// The using statement also closes the StreamReader.
using (StreamReader sr = new StreamReader(this.FilePath))
{
String line;
string[] fields;
try
{
// Read extents but don't use
line = sr.ReadLine();
// Get the overlap
line = sr.ReadLine();
OverLapMicrons = Convert.ToDecimal(line);
// Get the number of frames in each direction
line = sr.ReadLine();
fields = line.Split('\t');
info.WidthInTiles = Convert.ToInt32(fields[0], CultureInfo.InvariantCulture);
info.HeightInTiles = Convert.ToInt32(fields[1], CultureInfo.InvariantCulture);
// Get the microns per pixel factor
line = sr.ReadLine();
info.OriginalPixelsPerMicron = Convert.ToDouble(line, CultureInfo.InvariantCulture);
// By definition Ros's TileLoadInfo files consist of correlated data.
info.IsCorrelated = true;
// Get the extension of the files
line = sr.ReadLine();
filesInDir = new FileInfo[info.NumberOfTiles];
count = 0;
while ((line = sr.ReadLine()) != null)
{
fields = line.Split('\t');
tilePositions.Add(new TilePosition(fields[0],
Convert.ToInt32(fields[1], CultureInfo.InvariantCulture),
Convert.ToInt32(fields[2], CultureInfo.InvariantCulture)));
filesInDir[count++] = new FileInfo(this.DirectoryPath
+ "\\" + fields[0]);
}
}
catch (IOException e)
{
System.Windows.Forms.MessageBox.Show("Cannot parse file: " + e.Message);
}
}
Tile.IsCompositeRGB = false;
count = 0;
int width = 0;
int height = 0;
int bpp = 8;
FREE_IMAGE_TYPE type = FREE_IMAGE_TYPE.FIT_BITMAP;
// Find the first tile that exists to get the sizes and color depth etc
// but check all
bool oneNotFound = false, atLeastOneFound = false;
foreach (FileInfo file in filesInDir)
{
if (System.IO.File.Exists(file.FullName))
{
if (!atLeastOneFound)
{
FreeImageAlgorithmsBitmap fib = Tile.LoadFreeImageBitmapFromFile(file.FullName);
width = fib.Width;
height = fib.Height;
bpp = fib.ColorDepth;
type = fib.ImageType;
fib.Dispose();
// Set the overlap percentage
double widthInMicrions = width / info.OriginalPixelsPerMicron;
double heightInMicrions = height / info.OriginalPixelsPerMicron;
info.OverLapPercentageX =
(double)((double)OverLapMicrons / widthInMicrions) * 100.0;
info.OverLapPercentageY =
(double)((double)OverLapMicrons / heightInMicrions) * 100.0;
atLeastOneFound = true;
}
}
else
{
oneNotFound = true;
}
}
if (!atLeastOneFound) // No images at all!
{
throw (new MosaicReaderException("No images found."));
}
if (oneNotFound)
{
MessageBox.Show("At least 1 image is missing from the mosaic.", "Warning", MessageBoxButtons.OK, MessageBoxIcon.Warning);
}
foreach (FileInfo file in filesInDir)
{
if (this.ThreadController.ThreadAborted)
{
return;
}
if (!this.AllowedExtensions.Contains(file.Extension))
{
continue;
}
Point position = new Point();
position.X = tilePositions[count].X;
position.Y = tilePositions[count].Y;
Tile tile = new Tile(file.FullName, position, width, height);
tile.Width = width;
tile.Height = height;
tile.ColorDepth = bpp;
tile.FreeImageType = (FREE_IMAGE_TYPE)type;
info.Items.Add(tile);
count++;
}
}
