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Commit 866cf27a authored by Christopher Schmied's avatar Christopher Schmied
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Fixed bug in channel selection of registration and timelapse registration

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spim_registration/timelapse/registration.bsh
+ 73
− 84
View file @ 866cf27a
......@@ -117,16 +117,33 @@ String[] threshold_token = reg_threshold.split(delims);
String channel_string = "";
String processing_channel_string = "";
StringBuilder channel_string_multi = new StringBuilder();
// If there are no channels set returns an error
if (channels.equalsIgnoreCase(""))
{
System.out.println("Warning: There are no channels set");
}
// Returns an Error if there is one channel in channels but multiple settings in radius and or threshold
else if ( channel_token.length == 1 && (radius_1_token.length > 1 || radius_2_token.length > 1 || threshold_token.length > 1 ) )
{
System.out.println( "Error: Only one channel detected but multiple channel settings for radius or threshold" );
}
// Assembles String for Singel Channel
else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length == 1 )
{
processing_channel_string = "";
channel_string_multi.append("");
channel_string = "interest_point_specification=[Advanced ...] " +
"radius_1=" + reg_radius_1 + " " +
"radius_2=" + reg_radius_2 + " " +
"threshold=" + reg_threshold + " " +
"find_maxima";
}
// Dual Channels both Channels contain beads
else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length > 1 )
{
// Assembles String using StringBuilder for 2 Channels
for (int channel=0; channel < channel_token.length; channel++ )
......@@ -140,41 +157,22 @@ else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token
channel_string_multi.append(" ");
}
}
// Returns an Error if there is one channel in channels but multiple settings in radius and or threshold
else if ( channel_token.length == 1 && (radius_1_token.length > 1 || radius_2_token.length > 1 || threshold_token.length > 1 ) )
{
System.out.println( "Error: Only one channel detected but multiple channel settings for radius or threshold" );
}
// Returns an Error if set to Dual Channel one Channel contains beads but there is only one channel in channels
else if ( reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && channel_token.length == 1 )
{
System.out.println( "Error: reg_process_channel or channels set incorrectly" );
}
// Assembles String for Singel Channel
else if (reg_process_channel.equalsIgnoreCase( "Single channel" ) && channel_token.length == 1 )
{
reg_process_channel = "All channels"; // Sets reprocess channel All channels
processing_channel_string = "";
channel_string_multi.append("");
channel_string = "interest_point_specification=[Advanced ...] " +
"radius_1=" + reg_radius_1 + " " +
"radius_2=" + reg_radius_2 + " " +
"threshold=" + reg_threshold + " " +
"find_maxima";
}
// Returns and Error if set to Dual Channel but there are multiple settings in radius and or threshold
// Returns and Error if set to Dual Channel processing one channel contains the beads but there are multiple settings in radius and or threshold
else if ( reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && (radius_1_token.length > 1 || radius_2_token.length > 1 || threshold_token.length > 1 ) )
{
System.out.println( "Error: You said you wanted to process only one channel but there are multiple settings for radius or threshold" );
}
}
// Assembles String for Dual Channel but only one Channel contains beads
else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && channel_token.length > 1)
else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && channel_token.length > 1)
{
channel_string_multi.append("");
processing_channel_string = "processing_channel=[channel " + reg_processing_channel + "] ";
......@@ -190,9 +188,10 @@ else
{
System.out.println( "Error: Incorrect settings" );
}
System.out.println( "Processing Channel = " + processing_channel_string );
System.out.println( "Channel String: " + channel_string );
System.out.println( reg_process_channel );
System.out.println( "Multi channel String: " + channel_string_multi );
// Channel Setting Registration
......@@ -207,72 +206,62 @@ reg_interest_points_channel = System.getProperty( "reg_interest_points_channel"
System.out.println( "reg_interest_points_channel = " + reg_interest_points_channel );
// Splits up channels, reg_interest_points_channel
String delims = "[,]";
String[] channel_token = channels.split(delims);
// String delims = "[,]";
// String[] channel_token = channels.split(delims);
// Splits up channels, reg_interest_points_channel
String[] interest_token = reg_interest_points_channel.split(delims);
String reg_single_channel_string ="";
StringBuilder reg_multi_channel_string = new StringBuilder();
// If there are no channels set returns an error
if (channels.equalsIgnoreCase(""))
{
System.out.println("Warning: There are no channels set");
}
// Returns Error if Single Channel selected but multiple settings in channels or reg_interest_points_channel
else if ( reg_process_channel.equalsIgnoreCase( "Single Channel" ) && (channel_token.length > 1 || interest_token.length > 1 ))
{
System.out.println( "Error: Single Channel selected but multiple settings in channls or reg_interest_points_channel" );
}
// Assembles string for Single Channel registration
else if (reg_process_channel.equalsIgnoreCase( "Single Channel" ) && channel_token.length == 1 && interest_token.length == 1 )
{
System.out.println("Warning: There are no channels set");
}
// Assembles string for Single Channel registration
else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length == 1 && interest_token.length == 1 )
{
reg_multi_channel_string.append( "" );
reg_single_channel_string = "interest_points_channel_" + channels + "=" + reg_interest_points_channel + " ";
}
// Returns error if Multi Channels are selected but not enough settings in channels or reg_interest_points_channel
else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && ( channel_token.length < 1 || interest_token.length < 1) )
{
System.out.println( "Error: Multi Channel selected but only one setting in channels or reg_interest_points_channel" );
}
// Assembles string for Multi Channel registration
else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length > 1 )
{
for (int channel=0; channel < channel_token.length; channel++ )
{
reg_multi_channel_string.append( "" );
reg_process_channel = "All channels"; // Sets reprocess channel to all channels
reg_single_channel_string = "interest_points_channel_" + channels + "=" + reg_interest_points_channel + " ";
}
// Returns error if Multi Channels are selected but not enough settings in channels or reg_interest_points_channel
else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && ( channel_token.length < 1 || interest_token.length < 1) )
{
System.out.println( "Error: Multi Channel selected but only one setting in channels or reg_interest_points_channel" );
}
// Assembles string for Multi Channel registration
else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length > 1 )
{
for (int channel=0; channel < channel_token.length; channel++ )
{
String channel_part = "interest_points_channel_" + channel_token[channel] + "=" + interest_token[channel] + " ";
reg_multi_channel_string.append( channel_part );
reg_multi_channel_string.append(" ");
}
String channel_part = "interest_points_channel_" + channel_token[channel] + "=" + interest_token[channel] + " ";
reg_multi_channel_string.append( channel_part );
reg_multi_channel_string.append(" ");
}
}
// Returns error of Multi Channels one Channel contains the beads is selected but not enough settings in channels or reg_interest_points_channel
else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && ( channel_token.length < 1 || interest_token.length < 1 ))
{
System.out.println( "Error: Multi Channel one Channel contains beads selected but only one setting in channls or reg_interest_points_channel" );
}
// Assembles string for Multi Channel Processing one Channel Contains the beads
else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && channel_token.length > 1 && interest_token.length > 1)
{
for (int channel=0; channel < channel_token.length; channel++ )
{
String channel_part = "interest_points_channel_" + channel_token[channel] + "=" + interest_token[channel] + " ";
reg_multi_channel_string.append( channel_part );
reg_multi_channel_string.append(" ");
}
// Returns error of Multi Channels one Channel contains the beads is selected but not enough settings in channels or reg_interest_points_channel
else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && ( channel_token.length < 1 || interest_token.length < 1 ))
{
System.out.println( "Error: Multi Channel one Channel contains beads selected but only one setting in channls or reg_interest_points_channel" );
}
// Assembles string for Multi Channel Processing one Channel Contains the beads
else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && channel_token.length > 1 && interest_token.length > 1)
{
for (int channel=0; channel < channel_token.length; channel++ )
{
String channel_part = "interest_points_channel_" + channel_token[channel] + "=" + interest_token[channel] + " ";
reg_multi_channel_string.append( channel_part );
reg_multi_channel_string.append(" ");
}
}
System.out.println( "reg_single_channel_string = " + reg_single_channel_string );
System.out.println( "reg_multi_channel_string = " + reg_multi_channel_string );
System.out.println( "reg_single_channel_string = " + reg_single_channel_string );
System.out.println( "reg_multi_channel_string = " + reg_multi_channel_string );
// activate cluster processing
System.out.println( "=======================================================" );
......
spim_registration/timelapse/timelapse_registration.bsh
+ 40
− 53
View file @ 866cf27a
......@@ -86,66 +86,53 @@ System.out.println( "reg_interest_points_channel = " + reg_interest_points_chann
String delims = "[,]";
String[] channel_token = channels.split(delims);
String[] interest_token = reg_interest_points_channel.split(delims);
String reg_single_channel_string = "";
StringBuilder reg_multi_channel_string = new StringBuilder();
if (channels.equalsIgnoreCase(""))
{
System.out.println("Warning: There are no channels set");
}
// Returns Error if Single Channel selected but multiple settings in channels or reg_interest_points_channel
else if ( reg_process_channel.equalsIgnoreCase( "Single Channel" ) && (channel_token.length > 1 || interest_token.length > 1 ))
{
System.out.println( "Error: Single Channel selected but multiple settings in channls or reg_interest_points_channel" );
}
// Assembles string for Single Channel registration
else if (reg_process_channel.equalsIgnoreCase( "Single channel" ) && channel_token.length == 1 )
{
reg_multi_channel_string.append( "" );
reg_process_channel = "All channels"; // Sets reprocess channel to All channels
reg_single_channel_string = "interest_points_channel_" + channels + "=" + reg_interest_points_channel + " ";
}
// Returns error if Multi Channels are selected but not enough settings in channels or reg_interest_points_channel
else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && ( channel_token.length < 1 || interest_token.length < 1) )
{
System.out.println( "Error: Multi Channel selected but only one setting in channels or reg_interest_points_channel" );
}
// Assembles string for Multi Channel registration
else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length > 1 )
{
for (int channel=0; channel < channel_token.length; channel++ )
if (channels.equalsIgnoreCase(""))
{
System.out.println("Warning: There are no channels set");
}
{
String channel_part = "interest_points_channel_" + channel_token[channel] + "=" + interest_token[channel] + " ";
reg_multi_channel_string.append( channel_part );
reg_multi_channel_string.append(" ");
}
}
// Returns error of Multi Channels one Channel contains the beads is selected but not enough settings in channels or reg_interest_points_channel
else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && ( channel_token.length < 1 || interest_token.length < 1 ))
{
System.out.println( "Error: Multi Channel one Channel contains beads selected but only one setting in channls or reg_interest_points_channel" );
}
// Assembles string for Single Channel registration
else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length == 1 )
{
reg_multi_channel_string.append( "" );
reg_single_channel_string = "interest_points_channel_" + channels + "=" + reg_interest_points_channel + " ";
}
// Assembles string for Multi Channel Processing one Channel Contains the beads
else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && channel_token.length > 1 && interest_token.length > 1 )
{
for (int channel=0; channel < channel_token.length; channel++ )
{
String channel_part = "interest_points_channel_" + channel_token[channel] + "=" + interest_token[channel] + " ";
reg_multi_channel_string.append( channel_part );
reg_multi_channel_string.append(" ");
}
// Assembles string for Multi Channel registration
else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length > 1 )
{
for (int channel=0; channel < channel_token.length; channel++ )
{
String channel_part = "interest_points_channel_" + channel_token[channel] + "=" + interest_token[channel] + " ";
reg_multi_channel_string.append( channel_part );
reg_multi_channel_string.append(" ");
}
}
// Returns error of Multi Channels one Channel contains the beads is selected but not enough settings in channels or reg_interest_points_channel
else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && ( channel_token.length < 1 || interest_token.length < 1 ))
{
System.out.println( "Error: Multi Channel one Channel contains beads selected but only one setting in channls or reg_interest_points_channel" );
}
}
// Assembles string for Multi Channel Processing one Channel Contains the beads
else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && channel_token.length > 1 && interest_token.length > 1 )
{
for (int channel=0; channel < channel_token.length; channel++ )
{
String channel_part = "interest_points_channel_" + channel_token[channel] + "=" + interest_token[channel] + " ";
reg_multi_channel_string.append( channel_part );
reg_multi_channel_string.append(" ");
}
}
System.out.println( "reg_single_channel_string = " + reg_single_channel_string );
System.out.println( "reg_multi_channel_string = " + reg_multi_channel_string );
......
spim_registration/timelapse/tomancak_test_cluster.yaml
+ 1
− 1
View file @ 866cf27a
......@@ -50,7 +50,7 @@ resave_hdf5: {
registration: {
# "Single Channel" is not a valid choice for "Process_channel"
reg_process_channel: '"Single channels"',
reg_process_channel: '"All channels"',
reg_processing_channel: '"green"',
reg_interest_points_channel: '"beads"',
reg_radius_1: '2',
......
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