Update July-7 2017

UP-RS-ESP · Jul 7, 2017 · 5f8f1c0 · 5f8f1c0
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diff --git a/KZ-Picker/Matlab/DEM_MAT_parameters.mat b/KZ-Picker/Matlab/DEM_MAT_parameters.mat
diff --git a/KZ-Picker/Matlab/E_KZ_knickzone_selection.m b/KZ-Picker/Matlab/E_KZ_knickzone_selection.m
@@ -1,6 +1,14 @@
 %% Select Knickzones Using the Chi and Elevation Information from each Basin
 
+mkdir maps_and_chi_plots;
+mkdir csv_KZ_databases;
+
 fprintf(1,'step 4 of 4: Selecting Knickzones' )
+try
+    number_of_basins = length(basin_index);
+catch ME
+    number_of_basins = 1;
+end
 
 for i = 1:number_of_basins
     % record the maximum elevation of the entire streamobj (needed for
@@ -283,7 +291,7 @@
         %% New function interpolates chi-elev data
             % interpolates the points in the chiplot because the chi 
             % values do not increase with constant intervals between 
-            % successive values.  You shouldnt use a Savitzky Golay 
+            % successive values.  You shouldn�t use a Savitzky Golay 
             % filter on data that has a different stepsize between data
             % values, so the data must be interpolated over a constant 
             % measurement interval
@@ -859,14 +867,14 @@
         % specify filename for knickzone lips
         kp_lips_fn = strcat('kp_lips_basin', str_basin_id,'.csv');             
         %give filename
-        cd([oldfolder,'\csv_KZ_databases\'])
+        cd([oldfolder,'/csv_KZ_databases/'])
         fid = fopen(kp_lips_fn, 'w');
         fprintf(fid, txt);
         fclose(fid);
 
         % write .csv file containing knickzone lip information for
         % current parameters (need one row offset for the header)
-        dlmwrite([oldfolder,'\csv_KZ_databases\',kp_lips_fn],Knickpoint_Database_Lips_CB,'-append','delimiter',',', 'precision', '%.5f','roffset',1);
+        dlmwrite([oldfolder,'/csv_KZ_databases/',kp_lips_fn],Knickpoint_Database_Lips_CB,'-append','delimiter',',', 'precision', '%.5f','roffset',1);
 
         % specify filename for knickzone bases
         kp_bases_fn = strcat('kp_bases_basin', str_basin_id,'.csv');             
@@ -878,7 +886,7 @@
 
         % write .csv file containing knickzone lip information for
         % current parameters
-        dlmwrite([oldfolder,'\csv_KZ_databases\',kp_bases_fn],Knickpoint_Database_Bases_CB,'-append','delimiter',',', 'precision', '%.5f','roffset',1);
+        dlmwrite([oldfolder,'/csv_KZ_databases/',kp_bases_fn],Knickpoint_Database_Bases_CB,'-append','delimiter',',', 'precision', '%.5f','roffset',1);
 
         cd(oldfolder); % return to working directory
     end
@@ -911,14 +919,14 @@
 % specify filename for knickzone lips
 kp_lips_fn = strcat('kz_lips_all','.csv');             
 %give filename
-cd([oldfolder,'\csv_KZ_databases\'])
+cd([oldfolder,'/csv_KZ_databases/'])
 fid = fopen(kp_lips_fn, 'w');
 fprintf(fid, txt);
 fclose(fid);
 
 % write .csv file containing knickzone lip information for
 % current parameters (need one row offset for the header)
-dlmwrite([oldfolder,'\csv_KZ_databases\',kp_lips_fn],Knickpoint_Database_Lips,'-append','delimiter',',', 'precision', '%.5f','roffset',1);
+dlmwrite([oldfolder,'/csv_KZ_databases/',kp_lips_fn],Knickpoint_Database_Lips,'-append','delimiter',',', 'precision', '%.5f','roffset',1);
 
 % specify filename for knickzone bases
 kp_bases_fn = strcat('kp_bases_all','.csv');             
@@ -930,7 +938,7 @@
 
 % write .csv file containing knickzone lip information for
 % current parameters
-dlmwrite([oldfolder,'\csv_KZ_databases\',kp_bases_fn],Knickpoint_Database_Bases,'-append','delimiter',',', 'precision', '%.5f','roffset',1);
+dlmwrite([oldfolder,'/csv_KZ_databases/',kp_bases_fn],Knickpoint_Database_Bases,'-append','delimiter',',', 'precision', '%.5f','roffset',1);
 
 cd(oldfolder); 
 
diff --git a/KZ-Picker/Matlab/E_calib_KZ_calibration_I.m b/KZ-Picker/Matlab/E_calib_KZ_calibration_I.m
@@ -34,13 +34,19 @@
 mkdir calib_database_outputs;
 
 num = 1; %counter
+number_of_iterations = length(min_kp_size2_calib)*length(min_kp_size1_calib)*length(lumping_search_distance_calib)*length(SG_smoothing_calib);
+fprintf('At iteration # of %d: ', number_of_iterations);
 
 for b = 1:length(min_kp_size2_calib) % minimum knickpoint size2
     for a = 1:length(min_kp_size1_calib) % minimum knickpoint size1
         for c = 1:length(lumping_search_distance_calib)  % lumping window
             for l = 1:length(SG_smoothing_calib)   % smoothing window
+                fprintf('%d, ', num);
+                if mod(num,25) == 0
+                    fprintf('\nAt iteration # of %d: ', number_of_iterations);
+                end
 
-            iteration_number = num % tells you progress (this takes a while)
+            iteration_number = num; % tells you progress (this takes a while)
 
             %% Name Parameters
 
@@ -362,9 +368,6 @@
                 beta_all_tribs_all_basins{1} = beta_all_tribs;  % for each basin
             end
 
-
-            fprintf('\n');
-
             % All the knickpoints are saved in the above cell arrays
             % Organize all knickpoints into a lists (unpack the cell arrays and
             % organize these attributes into columns in a matrix so they 
@@ -506,7 +509,7 @@
                 kp_plot_size KZ_calib_northing_column_num KZ_calib_easting_column_num...
                 KZ_calib_relief_column_num do_you_have_calibration_KZ_bases smoothing_option...
                 theta_bf_option theta_ref num theta_bf ks_chiplot ksn_SA_store Min_DA_threshold...
-                Knickpoint_Database_Lips_all_params Knickpoint_Database_Bases_all_params...
+                Knickpoint_Database_Lips_all_params Knickpoint_Database_Bases_all_params orgfolder number_of_iterations oldfolder...
 
             end
         end

diff --git a/KZ-Picker/Matlab/F_calib_KZ_calibration_comparison_II.m b/KZ-Picker/Matlab/F_calib_KZ_calibration_comparison_II.m
@@ -89,7 +89,7 @@
 format long g
 
 % set current directory as 'oldfolder'
-oldfolder = pwd;
+oldfolder = orgfolder;
 
 % load attribute table for the calibration knickzone bases and lips. ROW 1
 % is assumed to be the header! so starts reading at ROW 2!!!!!!

diff --git a/KZ-Picker/Matlab/F_calib_KZ_calibration_comparison_II_only_calib_lips.m b/KZ-Picker/Matlab/F_calib_KZ_calibration_comparison_II_only_calib_lips.m
@@ -92,6 +92,7 @@
 format long g
 
 % set current directory as 'oldfolder'
+oldfolder = orgfolder;
 
 % load attribute table for the calibration knickzone lips. ROW 1
 % is assumed to be the header! so starts reading at ROW 2!!!!!!

diff --git a/KZ-Picker/Matlab/MASTER_RUN_KZ.m b/KZ-Picker/Matlab/MASTER_RUN_KZ.m
@@ -149,7 +149,7 @@
 %getting latest topotoolbox from: https://github.com/wschwanghart/topotoolbox
 %git clone https://github.com/wschwanghart/topotoolbox
 %!adjust the following to match your location!
-addpath('/home/bodo/Dropbox/Matlab-work/topotoolbox','genpath')
+addpath(genpath('/home/bodo/Dropbox/Matlab-work/topotoolbox'))
 
 %getting latest KZ-Picker code from https://github.com/UP-RS-ESP/DEM-KZP/tree/master/KZ-Picker/Matlab
 %git clone https://github.com/UP-RS-ESP/DEM-KZP/tree/master/KZ-Picker/Matlab
@@ -167,45 +167,43 @@
 %change to directory with data and start processing
 cd /home/bodo/Dropbox/Matlab-work/KZP-examples/SCI-1m-smugglers
 %extract archive
-!7z e smugglers_1m.7z
+%!7z x smugglers_1m.7z
+orgfolder = pwd;
 
 A_KZ_topometrics_1load_v1
 
 %% (2) Calculate flow direction and flow accumulation and choose basins to analyze
 %
-% (REQUIRES USER INPUT)
 B_KZ_topometrics_2preprocessing_v1
 
 %% (3) Mask DEM according to drainage basins selected for processing
-
+% (REQUIRES USER INPUT)
+%
 C_KZ_drainage_basin_plot_and_select
 
 %% (4) Use selections from data cursor to mask draiange basins of interest 
 % Calculate Ksn and Chi coordinate for stream-cell in each drainage basin
 % Export slope-area figures
 D_KZ_masking_DBs
 
-%% (5-Calibration) If calibration option is selected (NOTE: THIS STEP IS SLOW!)
+%% (5-Calibration) If calibration option is selected (NOTE: THIS STEP IS SLOW AND USUALLY ONLY NEEDS TO BE RUN ONCE!)
+oldfolder = orgfolder;
 
-oldfolder = pwd;
 if Calibration_option == 1
     % run calibration scripts and do not run the processing scripts
     E_calib_KZ_calibration_I
 
-        if do_you_have_calibration_KZ_bases == 1
-
+    if do_you_have_calibration_KZ_bases == 1
         F_calib_KZ_calibration_comparison_II
-
-        else
-
+    else
         F_calib_KZ_calibration_comparison_II_only_calib_lips
-
-        end
-
+    end
 end
 
 %% if calibration is not selected (default) run processing scripts with
 % default/inputted smoothing parameters
+%NOTE: The example calibrates the data and DOES NOT run the knickzone
+%detection. Set Calibration_option = 0 to run the knickzone detection
 if Calibration_option == 0
     % (5) Select Knickzones in each drainage basin
     % Select knickzones from Chi/elev data of each stream and tributary

diff --git a/KZ-Picker/Matlab/code_workflow.pdf b/KZ-Picker/Matlab/code_workflow.pdf
diff --git a/KZ-Picker/Matlab/code_workflow.pptx b/KZ-Picker/Matlab/code_workflow.pptx
diff --git a/KZ-Picker/Readme.md b/KZ-Picker/Readme.md
@@ -6,7 +6,7 @@ Neely, A., Bookhagen B., Burbank, D.W. (2017): An automated knickzone selection
 http://onlinelibrary.wiley.com/doi/10.1002/2017JF004250/full
 
 Code developed by Al Neely ([email protected]) and Bodo Bookhagen ([email protected])
-Latest update: 7-July-2017
+Latest update: 7-July-2017 (BB)
 
 The code was tested on a Ubuntu 16.04 LTS and Windows 7 operating system with Matalb R2015a and Matlab R2016b
 
@@ -23,9 +23,13 @@ Before running the code, you will need to install the additional items:
 
 1. Edit the 'PARAMETERS_INPUTS_KZ_picker' to set input and output filenames. Then use MASTER_RUN_KZ.m to process the DEM. There are additional information in the beginning of the MASTER_RUN_KZ.m file.
 
+There is a set of files generated that can be loaded in ArcMap/QGIS or a similar GIS.
+
+
 ## Examples
-There exists an example dataset at containing a 1-m DEM of a part of Santa Cruz Island, southern California: smugglers_1m_dem.
-This example file is available at https://www.dropbox.com/s/kpujj3mfezzd34b/smugglers_1m.7z?dl=0 or https://boxup.uni-potsdam.de/index.php/f/38152339
+There exists an example dataset at containing a 1-m DEM of a part of Santa Cruz Island, southern California: _smugglers_1m_dem.7z_.
+This example GeoTIF file is available at https://www.dropbox.com/s/kpujj3mfezzd34b/smugglers_1m.7z?dl=0 or https://boxup.uni-potsdam.de/index.php/f/38152339
+
 
 ## Additional information
 BEFORE using your DEM with this script, make sure that you use a projected coordinate system. We strongly suggest to use an UTM or other