diff --git a/spim_registration/timelapse/registration.bsh b/spim_registration/timelapse/registration.bsh
index 0031b54f98e3fb144fa2cf113fbb268728e9a6aa..d6872232b191687a082c3e8f591979528318672e 100755
--- a/spim_registration/timelapse/registration.bsh
+++ b/spim_registration/timelapse/registration.bsh
@@ -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( "=======================================================" );
diff --git a/spim_registration/timelapse/timelapse_registration.bsh b/spim_registration/timelapse/timelapse_registration.bsh
index bd60d18fe0a27480024ec8d04af45b66b6a5fddd..82c051815af93ceee782daab02e48dd8c0f7abc2 100755
--- a/spim_registration/timelapse/timelapse_registration.bsh
+++ b/spim_registration/timelapse/timelapse_registration.bsh
@@ -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 );
diff --git a/spim_registration/timelapse/tomancak_test_cluster.yaml b/spim_registration/timelapse/tomancak_test_cluster.yaml
index 392954fa193b4afcc771e1e4e68b76f9cdf0a27c..77c76210cd21385a3cbff9cf250fd1a697657831 100755
--- a/spim_registration/timelapse/tomancak_test_cluster.yaml
+++ b/spim_registration/timelapse/tomancak_test_cluster.yaml
@@ -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',