update to process run 129 & 130

leewujung · May 15, 2018 · 4cf645e · 4cf645e
1 parent 460b834
commit 4cf645e
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Showing 5 changed files with 93 additions and 28 deletions.
diff --git a/echo_info_fcn.m b/echo_info_fcn.m
@@ -8,6 +8,8 @@
 %             use SL to calibrate the spectrum
 %             save info extracted for each ping
 % 2017 01 25  Clean up code to work with new beamforming results
+% 2018 05 15  Add exceptions for missing SL data (run 130 before
+%             ping 95 is not usable)
 
 
 function echo_info_fcn(data_path,ping_num,base_save_path,base_data_path,plot_show_opt)
@@ -139,14 +141,19 @@ function echo_info_fcn(data_path,ping_num,base_save_path,base_data_path,plot_sho
     % Get SL for spectral calibration
     SL = get_SL(run_num,ping_num_curr);
 
-    % Get raw echo spectrum (without any compensation)
-    no_spec = get_spectrum_mtm(no,A.data.sample_freq,win_perc);
-    wr_spec = get_spectrum_mtm(wr,A.data.sample_freq,win_perc);
-
-    % Compensation for all factors 
-    no_spec = compensate_echo_spectrum(no_spec,SL,A);
-    wr_spec = compensate_echo_spectrum(wr_spec,SL,A);
+    if ~isempty(SL)
+        % Get raw echo spectrum (without any compensation)
+        no_spec = get_spectrum_mtm(no,A.data.sample_freq,win_perc);
+        wr_spec = get_spectrum_mtm(wr,A.data.sample_freq,win_perc);
 
+        % Compensation for all factors 
+        no_spec = compensate_echo_spectrum(no_spec,SL,A);
+        wr_spec = compensate_echo_spectrum(wr_spec,SL,A);
+    else
+        no_spec = [];
+        wr_spec = [];
+    end
+
     % Get echo stat
     no_env = mf_env.env(no_r_idx(1):no_r_idx(2),no_a_idx(1):no_a_idx(2));
     wr_env = mf_env.env(wr_r_idx(1):wr_r_idx(2),wr_a_idx(1):wr_a_idx(2));
@@ -217,24 +224,26 @@ function echo_info_fcn(data_path,ping_num,base_save_path,base_data_path,plot_sho
     set(gca,'fontsize',12,'xtick',[1e4,1e6,1e8])
     hold off
     grid
-
-    subplot(133)  % spectrum
-    cla
-    plot(no_spec.freq_vec/1e3,no_spec.pxx_dB_mean_comp,...
-        'color',corder(1,:),'linewidth',2);
-    hold on
-    plot(wr_spec.freq_vec/1e3,wr_spec.pxx_dB_mean_comp,...
-        'linewidth',2,'color',[153,204,255]/255);
-    ll = legend('no wreck','wreck');
-    set(ll,'fontsize',11,'location','southoutside')
-    ylim([-140 -100])
-    xlim([1.6 3.8])
-    xlabel('Frequency (kHz)','fontsize',14)
-    ylabel('Spectral density (dB/Hz)','fontsize',14)
-    set(gca,'fontsize',12,'xtick',1.6:0.4:3.8,'ytick',-140:10:-100)
-    grid on
-    box on
 
+    if ~isempty(SL)
+        subplot(133)  % spectrum
+        cla
+        plot(no_spec.freq_vec/1e3,no_spec.pxx_dB_mean_comp,...
+             'color',corder(1,:),'linewidth',2);
+        hold on
+        plot(wr_spec.freq_vec/1e3,wr_spec.pxx_dB_mean_comp,...
+             'linewidth',2,'color',[153,204,255]/255);
+        ll = legend('no wreck','wreck');
+        set(ll,'fontsize',11,'location','southoutside')
+        ylim([-140 -100])
+        xlim([1.6 3.8])
+        xlabel('Frequency (kHz)','fontsize',14)
+        ylabel('Spectral density (dB/Hz)','fontsize',14)
+        set(gca,'fontsize',12,'xtick',1.6:0.4:3.8,'ytick',-140:10:-100)
+        grid on
+        box on
+    end
+
     mtit(title_text,'fontsize',16);
 
     saveSameSize_150(gcf,'file',fullfile(save_path,[save_fname,'.png']),...

diff --git a/echo_info_fcn_runner.m b/echo_info_fcn_runner.m
@@ -1,6 +1,10 @@
 % 2018 01 13  Run echo_info_fcn in batch
+% 2018 05 15  Run echo_info_fcn on Run 130 and 129 --> these are
+%             before dusk sessions to figure out how fluctuation
+%             shown in the beginning of Run 131
 
-run_num_all = [131,79,87,94,103,115,120,124];
+%run_num_all = [131,79,87,94,103,115,120,124];
+run_num_all = [130,129];
 
 base_data_path = '~/internal_2tb/trex/figs_results/';
 base_save_path = '~/internal_2tb/trex/figs_results/';
@@ -49,6 +53,18 @@
             wfm1 = 1;
             wfm2 = 2;
             data_path = 'subset_beamform_cardioid_coherent_run124';
+          case 129
+            ping_num1 = 1:2:210;    % run 129
+            ping_num2 = 2:2:210;    % run 129
+            wfm1 = 1;
+            wfm2 = 2;
+            data_path = 'subset_beamform_cardioid_coherent_run129';
+          case 130
+            ping_num1 = 1:2:170;    % run 130
+            ping_num2 = 1:2:170;    % run 130
+            wfm1 = 1;
+            wfm2 = 2;
+            data_path = 'subset_beamform_cardioid_coherent_run130';
           case 131
             ping_num1 = 1:2:1000;    % run 131
             ping_num2 = 2:2:1000;    % run 131

diff --git a/get_SL.m b/get_SL.m
@@ -5,6 +5,8 @@
 % 2016 11 21
 % 2017 01 23  Clean up
 % 2017 02 19  Enable loading each individual MON file for each ping
+% 2018 05 15  Add files for run 129 & 130
+%             Note exception for run 130 --don't process ping_num<95
 
 % Load transmit waveform
 if isunix
@@ -28,10 +30,27 @@
     amp_mon_subpath = 'TREX13_MON_13-05-14_21-27-37-260';
   case 124
     amp_mon_subpath = 'TREX13_MON_13-05-15_21-11-39-716';
+  case 129
+    amp_mon_subpath = 'TREX13_MON_13-05-16_14-59-11-817';
+  case 130
+    amp_mon_subpath = 'TREX13_MON_13-05-16_16-52-54-133';
   case 131
     amp_mon_subpath = 'TREX13_MON_13-05-16_18-28-07-368';
 end
-amp_mon_file = sprintf('TREX13_MON_I%05d_P%05d.mat',run_num,ping_num);
+if run_num==130
+    if ping_num < 95
+        S = [];
+        return
+    else
+        ping_num = ping_num-94;
+    end
+    amp_mon_file = sprintf('TREX13_MON_I%05d-restart_P%05d.mat',run_num,ping_num);
+elseif run_num==129
+    S = [];
+    return    
+else
+    amp_mon_file = sprintf('TREX13_MON_I%05d_P%05d.mat',run_num,ping_num);
+end
 
 A = load(fullfile(amp_mon_path,amp_mon_subpath,amp_mon_file));
 

diff --git a/subset_beamform_runner.m b/subset_beamform_runner.m
@@ -0,0 +1,19 @@
+% 2018 05 15  Make a runner script to extract and save a subset of
+%             beamformed data for faster access 
+
+
+addpath('~/code_matlab_dn/');
+addpath(['~/code_git/trex_fish/Triplet_processing_toolbox']);
+base_save_path = '~/internal_2tb/trex/figs_results/';
+base_data_path = '~/internal_2tb/trex/figs_results/';
+
+% Processing for run 130
+%data_path = 'beamform_cardioid_coherent_run130';
+%ping_num = 1:170;
+%subset_beamform_fcn(data_path,ping_num,base_save_path,base_data_path);
+
+% Processing for run 129
+data_path = 'beamform_cardioid_coherent_run129';
+ping_num = 1:210;
+subset_beamform_fcn(data_path,ping_num,base_save_path,base_data_path);
+
diff --git a/trex_fish_notes_2018.md b/trex_fish_notes_2018.md
@@ -126,14 +126,16 @@
 
 
 ************************************************
-## 2018/05/14
+## 2018/05/14-15
 ### Process run 129 and 130
 - Need to process these two runs to figure out why there was high Emax and SI in AW1 before dusk. Was this a pattern from earlier during the day?
 - May have to process data from other days before the overnight session to figure this out.
 - Run 129 and 130 used the same 2 waveforms as run 131, which is the expt session we focus analysis on for the ms.
   - Run 130: 170 pings
   - Run 129: 210 pings
-
+- Added `subset_beamform_runner` and updated `get_SL`, `echo_info_fcn`, `echo_info_fcn_runner` for processing these 2 runs.
+- Run 130 was stopped and restarted so there were some confusion of file numbers. Jie noted that there were 96 good files in run 130. This number is consistent with the number of files in the run 131 HAARI folder. But I decided to only use the last 76 files (ping 95-170) since I can be certain that these are the files that did not have problem after the system was restarted.
+- Run 129 HAARI folder is missing ping 131... added exceptions to `get_SL`.