Merge remote-tracking branch 'origin/master'

JavaSource/resources/ferret/scripts/LAS_annotations_xml.jnl

@@ -32,7 +32,8 @@ DEFINE SYMBOL out = <annotations>
 GO write_to_xml
 
 ! orthogonal axis labels
-IF `($longitude_lab%0|*>1%)+($latitude_lab%0|*>1%)+($depth_lab%0|*>1%)+($time_lab%0|*>1%)+($ens_lab%0|*>1%)+($forecast_lab%0|*>1%) GT 0` THEN \
+
+IF `($longitude_lab%0|*>1%)+($latitude_lab%0|*>1%)+($depth_lab%0|*>1%)+($time_lab%0|*>1%)+($year_lab%0|*>1%)+($ens_lab%0|*>1%)+($forecast_lab%0|*>1%) GT 0` THEN \
     GO annotation_orthogonal_axes 
 
 ! variable and dataset labels

JavaSource/resources/ferret/scripts/LAS_draw_multi_line_plot.jnl

@@ -69,8 +69,7 @@ IF `($have_multiline_defs"0|*>1") EQ 0` THEN
      LET title_len = `MAX(tlen, title_len)`;\
      DEFINE SYMBOL units_($qdat) = `UPCASE("($data_($qdat)_units)")`;\
      DEFINE SYMBOL all_units_same = `($all_units_same) AND (STRCMP("($units_0)", "($units_($qdat))") EQ 0)`;\
-     GO LAS_pp_set_region_labels \
-   )
+     GO LAS_pp_set_region_labels )
    DEFINE SYMBOL plot_vars_0 = ($plot_arg)
 
 ENDIF ! have_multiline_defs

JavaSource/resources/ferret/scripts/LAS_initial_setup.jnl

@@ -12,10 +12,6 @@
 
 SET MODE VERIFY:ALWAYS
 
-! Put into the debug output what PyFerret/Ferret is running, and when.
-
-SHOW SYMBOL ferret_version, ferret_platform, program_name, current_date
-
 DEFINE SYMBOL initialize_script_arg = ($1"2")
 
 ! Make sure to do the SET REDIRECT just once.
@@ -25,13 +21,24 @@ DEFINE SYMBOL initial_setup_done = 1
 
 ! Put the output into the log file so that FshowGO will list
 ! the tree of GO script calls.
-SET REDIRECT/APPEND/TEE/file="($result_debug_filename)" STDOUT,STDERR
+SET REDIRECT/CLOBBER/TEE/file="($result_debug_filename)" STDOUT,STDERR
+
+! Put into the debug output what PyFerret/Ferret is running, and when.
+
+SHOW SYMBOL ferret_version, ferret_platform, program_name, current_date
+SHOW MEMORY
 
 IF `($initialize_script_arg) EQ 0` THEN EXIT/SCRIPT
 
+! add the operation script name to the debug output.
+
+SAY
+SAY The operation script is ($operation_service_action)
+SAY
 
 IF ($program_name"0|PyFerret>1|*>0") THEN EXIT/SCRIPT
 
+
 ! Reset the default gif filename used internally by Ferret.
 ! This must be done before PPLUS is opened.  Some of the scripts use PPL
 ! symbol editing, so even before any plot commands are issued, pplus is 

JavaSource/resources/ferret/scripts/LAS_initialize_data.jnl

@@ -40,6 +40,6 @@ IF `($ferret_memory"25.6") LT 100` THEN SET MEM/SIZ=300
 ! If a Ferret property ferret_add_a_note is set, define a note that will
 ! be added to the annotations box. The note may contain a URL.
 
-GO LAS_note_from_property
+IF ($ferret_add_a_note"0|*>1") THEN GO LAS_note_from_property
 
 ! End of ------------LAS_initialize_data.jnl--------------------------

JavaSource/resources/ferret/scripts/LAS_initialize_feature_id.jnl

@@ -1,81 +1,62 @@
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 ! LAS_initialize_feature_id.jnl
+! ACM 8/2020 version for DSG datasets
 !
 ! Define variables and symbols based on feature (trajecotory or profile)
 ! identification variables
+! NOTE:  For trajectory set, the calculation of individual features only works if the 
+! NOTE:  intermediate netCDF files is ordered by feature_ID.  Make sure that
+! NOTE:  the SQL query ends with:  'ORDER BY feature_ID'.
+
 !
-! FEATURES      - unique identifier for each cruise
+! FEATURES      - unique identifier for each feature
 ! FEATURE_COUNTS - number of points per trajectory  Now use symbol rowvar
 
 IF ($nodata"0|*>1") THEN EXIT/SCRIPT
 IF `($ferret_memory"25.6") LT 200` THEN SET MEM/siz=200
 
 ! Create the 'feature_evnt' variable which increments for each new trajectory.
 
-! NOTE:  The calculation of individual cruises only works if the 
-! NOTE:  intermediate netCDF files is ordered by cruise_ID.  Make sure that
-! NOTE:  the SQL query ends with:  'ORDER BY cruise_ID'.
-
 DEFINE SYMBOL feature_max_labels = 200
-DEFINE SYMBOL numobs `($ferret_plot_var),return = isize`
-
 LET featurevar = ($rowvar)
-LET nfeatures = `featurevar,RETURN=($rind)size`
 
-!If undefined, set up the feature_numbers variable
-DEFINE AXIS/X=1:`nfeatures`:1 xfeature_axis
-
-IF `($have_feature_nums"0|*>1") EQ 0` THEN LET feature_numbers = x[gx=xfeature_axis]
+IF `($have_feature_nums"0|*>1") EQ 0` THEN LET feature_numbers = _m[ge=featurevar]
 
 ! rind is direction of rowsize, defined in feature_initialize
-LET longest = featurevar[($rind)=@max]+2
-
-LET data_var_c =  EXPNDI_BY_Z_COUNTS(longitude, xsequence(featurevar),`longest`)
-LET id_by_c =  EXPNDI_ID_BY_Z_COUNTS(xsequence(featurevar),`longest`)
+LET longest = `rowsize[e=@max]` + 2
 
 ! If dsg file then these symbols are set up.
 IF `($data_($num)_var"0|($feature_variable)>1|*>0") AND ($rowvar"0|*>1")` THEN 
-   LET data_var_id = EXPND_BY_LEN(feature_numbers,($rowvar), `($rowvar)[M=@sum]`)
-   IF ($feature_type"0|*>1") THEN SET VAR/TITLE="($feature_type) ID" data_var_id
-   DEFINE SYMBOL data_var = data_var_id
+   DEFINE SYMBOL data_var = feature_numbers
    EXIT/SCRIPT
 ENDIF
 
 IF `($its_prop_prop_plot"0|*>1") EQ 0` THEN
-   LET data_var_id = EXPND_BY_LEN(feature_numbers,XSEQUENCE(featurevar), `featurevar[M=@sum]`)
-   IF ($feature_type"0|*>1") THEN SET VAR/TITLE="($feature_type) ID" data_var_id
-   DEFINE SYMBOL data_var = data_var_id
-
+   DEFINE SYMBOL data_var = feature_numbers
    EXIT/SCRIPT
 ENDIF
 
-! If  a subset of cruise ids is given then only plot those on a Prop/Prop 
+! If  a subset of feature ids is given then only plot those on a Prop/Prop 
 ! plot, but using the symbols and colors as determined by the whole dataset.
 ! If given, traj_list is a list of numbers.
 
    IF ($ferret_traj_list"0|*>1") THEN
       LET subset_ids = {($ferret_traj_list)}
-      LET n_subset = `subset_ids,RETURN=isize`
 
 ! Define a mask to use on the entire list of values: plot or not to plot
 ! the polygons on the prop-prop plot.
 
       LET subm_ids = IF ELEMENT_INDEX(traj_numbers,subset_ids) THEN 1
       IF `($subset_mask"0|*>1") EQ 0` THEN LET subset_mask = subm_ids + 0*x[x=1:`ntrajs`]  ! put it on a non-abstract axis. 
-
-! apply mask as data_var_c* subset_mask
-
-      LET n_subset = `subset_mask[I=@NGD]`
-      DEFINE SYMBOL cruises_shown = `n_subset`
-      DEFINE SYMBOL prof_traj_shown = `n_subset`
+      SET DATA/FMASK=subset_mask ($num)
    ELSE
 
-! There may be a subset already defined from ferret_cruise_list
+! There may be a subset already defined from ferret_feature_list
 
       IF `($subset_mask"0|*>1") EQ 0` THEN LET subset_mask = 1 + 0*i[i=1:`nfeatures`]
 
       LET n_subset = `subset_mask[I=@NGD]`
-      DEFINE SYMBOL cruises_shown = `n_subset`
+      DEFINE SYMBOL features_shown = `n_subset`
       DEFINE SYMBOL prof_traj_shown = `n_subset`
    ENDIF
 

JavaSource/resources/ferret/scripts/LAS_insitu_waterfall_setup.jnl

@@ -0,0 +1,111 @@
+!!!!! LAS_insitu_waterfall_setup.jnl
+
+! Initialize the dataset and set up for profile plots from DSG 
+! datasets using native-DSG enabled Ferret. 
+! ACM 8/2020 version for DSG datasets
+
+GO LAS_initialize_region 0
+
+IF ($data_0_var"0|vid>1|*>0")  THEN
+   DEFINE SYMBOL  ferret_by_id = 1
+   USE "($data_0_url)"
+   LET varnames = ..varnames
+
+   DEFINE SYMBOL  data_0_var = `varnames[i=1]`
+   CANCEL DATA "($data_0_url)"
+ENDIF
+GO LAS_initialize_data 0
+
+! Check for errors (They often occur during dataset initialization.)
+
+IF ($error_status"0|*>1") THEN
+  MESSAGE/ERROR **ERROR ($error_string)
+  PROGRAM
+ENDIF
+
+! Find the xyzt variables 
+
+GO feature_get_direction_vars
+
+! Set the URL label for the first dataset.
+GO LAS_url_label 0
+
+! Create the profile variables and symbols
+
+DEFINE SYMBOL variable_lab = ($variable_lab) at depth (meters)
+
+! Set up to color by a feature-variable including possibly time
+
+IF `color_by_feature EQ 1 OR color_by_index EQ 1` THEN 
+   IF ($data_var"0|($data_t_var)>1|*>0") THEN DEFINE SYMBOL ferret_plot_key = date_key
+   IF `($data_var"0|($data_t_var)>1|*>0") EQ 0` THEN 
+      IF `($ferret_palette"0|*>1") EQ 0` THEN DEFINE SYMBOL ferret_palette = ten_by_levels
+      IF `($input_fill_levels"0|*>1") EQ 0` THEN DEFINE SYMBOL ferret_fill_levels = (1,($nfeatures),1)
+      DEFINE SYMBOL ferret_plot_title Colored by Profile Number
+   ENDIF 
+   GO LAS_initialize_feature_id
+ENDIF
+
+! Special color-by-time key
+IF ($ferret_plot_key"0|date_key>1|*>0") THEN GO setup_date_key.jnl 
+
+
+! For annotations in LAS_results.  If we are coloring by a
+! feature-variable then ngood = npts
+
+DEFINE SYMBOL dtype = `($data_var),return=dtype`
+IF `($dtype"0|CHAR>0|*>1") EQ 0` THEN
+   DEFINE SYMBOL error_string = Invalid data type for variable ($ferret_title_0). Choose another variable.
+   MESSAGE/ERROR **ERROR ($error_string)
+   EXIT/PROGRAM
+ENDIF
+
+DEFINE SYMBOL shape = `($data_var),RETURN=shape`
+IF ($shape"0|E>1|*>0") THEN 
+   DEFINE SYMBOL ngood_data = ($numobs)
+ELSE 
+   LET allgood = ($data_var)[($shape"x")=@ngd]
+   DEFINE SYMBOL ngood_data = `allgood[e=@sum]`
+   DEFINE SYMBOL nbad_data = `($numobs) - ($ngood_data)`
+ENDIF
+
+! Plot qualifiers (graticule lines etc)
+GO LAS_set_plot_qualifiers 
+
+! Open the window
+GO LAS_open_window
+
+! Turn on annotate_key, which persists until turned off
+! (unless key_annoatate property tells us otherwise).
+
+IF ($ferret_key_annotate"1|0|1|*>1") THEN
+   KEYMARK 1
+ELSE
+   KEYMARK 0
+ENDIF
+
+IF `($ribbon"1|0|1|*>1") AND ($ngood_data"0|0|*>1") GT 0`  THEN
+   DEFINE SYMBOL  qualifiers = ($qualifiers)/KEY
+ELSE
+   DEFINE SYMBOL  qualifiers = ($qualifiers)/NOKEY
+ENDIF
+
+DEFINE SYMBOL qualifiers = ($qualifiers)/LEVELS=($ferret_fill_levels"v")
+IF ($program_name"|PyFerret>1|*>0") THEN DEFINE SYMBOL qualifiers = ($qualifiers)/SYMBOL=boxfill
+
+IF ($ribbon"0|*>1") THEN \
+   DEFINE SYMBOL  plot_command = PLOT/VS/RIBBON/LINE($qualifiers)
+
+! Variables for the waterfall plots  ($data_var) , ($data_x_var), ($data_y_var), ($data_z_var), ($data_t_var)
+! ... apply masks here?
+!
+! LET/TITLE="Depth"/UNITS="m"  issurf =    ! Surface locations ... should be location x,y first element of each profile...
+
+DEFINE VIEWPORT/XLIM=0:1/YLIM=0:1 vfull1
+DEFINE VIEWPORT/XLIM=0:1/YLIM=0:1 vfull2
+
+DEFINE SYMBOL view1 = vfull1
+DEFINE SYMBOL view2 = vfull2
+
+! End of file ------------ LAS_insitu_waterfall_setup.jnl--------------------------
+

JavaSource/resources/ferret/scripts/LAS_insitu_write_webrowset.jnl

@@ -2,7 +2,7 @@
 ! LAS_insitu_write_webrowset.jnl
 !
 !
-! Make a LIST/QUIET of the ID number and Cruise ID to go back 
+! Make a LIST/QUIET of the ID number and Feature ID to go back 
 ! for possible subsets of this set of cruises.
 
 CANCEL MODE VERIFY
@@ -12,21 +12,22 @@ IF `($result_icon_webrowset_filename"0|*>1") EQ 0` THEN
   EXIT/SCRIPT
 ENDIF
 
-! Write all the counter numbers and the cruise IDs in the webrowset format.
-! For SOCAT 3, cruise_id cruise_name are identical to cruise_expocode
+IF ($subset_mask"0|*>1") THEN CANCEL DATA/FMASK 1
 
-IF ($feature_variable"0|*>1") THEN 
+! Write all the counter numbers and the cruise IDs in the webrowset format.
+! For SOCAT 3, feature_id feature_name are identical to expocode
 
-   let imask = i[gx=xmask_axis]
+IF ($feature_name"0|*>1") THEN 
 
-   let webrow_mask = XSEQUENCE(feature_mask)* imask
+   define axis/x=1:`nfeatures`:1 xaxtest
+   let imask = x[gx=xaxtest]
 
 ! What do we want here? write_webrow with imask would put out the full key,
 ! or write_webrow_icon with webrow_mask would make a subset key, listing names and numbers 1, 3, 5, ...
 
 ! If writing the whole key, we can use write_webrow:
 
-   LOAD write_webrow_gwt(XSEQUENCE(($feature_variable)), XSEQUENCE(($feature_variable)), XSEQUENCE(imask), "($result_icon_webrowset_filename)")
+   LOAD write_webrow_gwt(XSEQUENCE(($feature_name)), XSEQUENCE(($feature_name)), imask, "($result_icon_webrowset_filename)")
 
 ENDIF
 
@@ -39,7 +40,4 @@ IF ($debug_mode"0|*>1") THEN
    SAY ----- debug mode Webrowset xml ($secs) -----
 ENDIF
 
-
-!!!!
-
 ! End of file ------------ LAS_insitu_write_webrowset.jnl --------------------------

JavaSource/resources/ferret/scripts/LAS_is_range.jnl

@@ -4,27 +4,38 @@
 ! Given a min and max variables defined, see if they are valid data
 ! and use them to define axis min,max, delta. If min and max are not
 ! valid then return nominal 0:100 and set an error flag.
+! 8/19 *acm* more bad-value handling
 ! 2/25/2020 ACM robust method usin Ferret/PyFerret internal method 
 !           to set range for constant-valued data
 
 LET baddat = 0
 
 CANCEL SYMBOL dm_labels
 
-LET ok = IFV ($1) THEN 1 ELSE 0
+IF ($1"0|bad>1|*>0") THEN 
+   let ok = 0
+ELSE
+   LET ok = IFV (($1)) THEN 1 ELSE 0
+ENDIF 
+
 IF `ok` THEN 
    DEFINE SYMBOL ax_lo = `($1)`
 ELSE 
    DEFINE SYMBOl ax_lo = bad
 ENDIF
-LET ok = IFV ($2) THEN 1 ELSE 0
+
+IF ($2"0|bad>1|*>0") THEN 
+   let ok = 0
+ELSE
+   LET ok = IFV (($2)) THEN 1 ELSE 0
+ENDIF 
+
 IF `ok` THEN 
    DEFINE SYMBOL ax_hi = `($2)`
 ELSE 
    DEFINE SYMBOl ax_hi = bad
 ENDIF
 
-
 IF `($ax_lo"0|bad>1|*>0") OR ($ax_hi"0|bad>1|*>0")` THEN 
   LET ax_lo = 0
   LET amin = 0