Update readme

README.md

@@ -1,26 +1,8 @@
-## Update 11/21/2014
-Detector has been updated to accept .wav files in addition to x.wavs.
-If you run the detector on directories of wav files, it will look for file start time information in the file name.
-
-Edit the regular expression in the load settings scripts:
-
-parametersHR.DateRE = '_(\d*)_(\d*)';
-
-to match your filename date format. 
-
-The result should be a string of numbers in the following order:
-yyyymmddHHMMSS
-
-The implementation is a little bit wonky, so contact me if you have problems.
-
-The detector will determine what file type you're using, but to be on the safe side, I'd suggest analyzing wav and xwav files separately.
-
-
 # Density Estimation Detector
 
 Set of scripts to detect odontocete clicks above a threshold recieved level in .x.wav data. This two-pass detector is based on and incorporates previous work by Marie A. Roch, Simone Baumann-Pickering, and Sean M. Wiggins. 
-Detector by Kait E. Frasier.
 
+Detector by Kait E. Frasier.
 
 
 ## How To Use This Code:
@@ -37,15 +19,23 @@ Detector by Kait E. Frasier.
 
 ```matlab
 % Set transfer function location
-tfFullFile = 'E:\Code\TF_files\585_091116_invSensit_MC.tf';
- 
-% Location of files to be analyzed
+tfFullFile = 'E:\Code\TF_files\Recalculated\tf files\740_140303\740_140303_invSensit.tf';
+% Note, if you don't have a transfer function just use:
+% tfFullFile = [];
+
+% Location of base directory containing directories of files to be analyzed
 baseDir = 'H:\';
- 
-% Name of the deployment. This should be the first few characters in the
-% names of the xwav files you want to look at.
-depl = 'GofMX';
- 
+
+% Optional output directory location. Metadata directory will be created in outDir
+% if specified, otherwise it will be created in baseDir.
+% outDir = '<your path here>';
+outDir  = 'I:\DCL\WAT_NC_'; 
+
+% Name of the deployment. This should be the first few characters in the 
+% directory(ies) you want to look in you want to look at. For now, 
+% directory hierarchy is expected to be: basedir>depl*>*.x.wav
+depl = 'WAT_NC_';
+
 % Set flags indicating which routines to run. 
 lowResDet = 1; %run short time detector.
 highResDet = 1; %run high res detector
@@ -54,16 +44,28 @@ highResDet = 1; %run high res detector
 
 * NOTE: The high res detector relies on output from the low res step, but once you've run the low res, you don't need to re-run it, unless you change your parameters.
 
+5. If you want to restrict the detector to only look at certain time periods, you can do so using a spreadsheet of start and end times specified in de_detector.m 
+
+```matlab
+%%%% Optional: guided detection spreadsheet, can be empty
+gDxls = 'E:\Data\John Reports\DCLDEdata\WAT_NC_guidedDets.xlsx';
+% gDxls = []; % if not used
+```
+
+## For .wav files
 
-## Things to know
+If you run the detector on directories of wav files, it will look for file start time information in the file name.
+
+Edit the regular expression in the load settings scripts:
 
- - This detector is set up to run without manual detection inputs. Adding the option to choose times based on a manual pass is trivial, but not currently implemented.
+parametersHR.DateRE = '_(\d*)_(\d*)';
 
-- .wav file inputs are not currently supported.
+to match your filename date format. 
 
-- Currently optimized for dolphins in the Gulf of Mexico. Use cautiously, especially if adapting to other odontocetes. 
+The result should be a string of numbers in the following order:
+yyyymmddHHMMSS
 
-- In noisy areas, a more restrictive postprocessing step is possible. Email for more info.
+The detector will determine what file type you're using, but to be on the safe side, I'd suggest analyzing wav and xwav files separately.
 
 
 ## Outputs