Merge remote-tracking branch 'origin/devel' into MMSdevel

.github/CONTRIBUTING.md

@@ -13,7 +13,7 @@ If working on a special development branch (e.g. [MMSdevel](https://github.com/i
 
 1. According to [Matlab Style Guidelines](https://web.archive.org/web/20210424065750/http://www.datatool.com/downloads/matlab_style_guidelines.pdf "MATLAB Programming Style Guidelines")
 2. Help follows matlab style, see [irf_template.m](https://github.com/irfu/irfu-matlab/blob/master/irf/irf_template.m)
-3. Matlab code files checked for possible problems, using [checkcode](https://www.mathworks.com/help/matlab/ref/checkcode.html)
+3. Matlab code files checked for possible problems, using [checkcode](https://www.mathworks.com/help/matlab/ref/checkcode.html) (or [codeIssues](https://www.mathworks.com/help/matlab/ref/codeissues.html) if using a modern Matlab release).
 4. For new code written, use only two spaces as indentation.
 
 ## Git

.github/pom.xml

@@ -11,7 +11,7 @@
     <dependency>
       <groupId>org.xerial</groupId>
       <artifactId>sqlite-jdbc</artifactId>
-      <version>3.43.0.0</version>
+      <version>3.44.0.0</version>
     </dependency>
     <!-- https://github.com/PRBEM/IRBEM -->
     <dependency>

.gitignore

@@ -1,6 +1,7 @@
 *.m~
 *.DS_Store
 *.asv
+*.swp
 fort.6
 .caa.log
 # Path for report (created by tests_before_release.m)

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
 
   ## Some pre-commit out-of-the-box hooks
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: "v4.4.0"
+    rev: "v4.5.0"
     hooks:
       - id: check-case-conflict
       - id: check-json

mission/cluster/caa/caa-control/Makefile

@@ -6,21 +6,21 @@ XSLTPROC=xsltproc
 all: html txt cef
 
 html: check ns_ops_epo.xml
-	${XSLTPROC} html.xsl ns_ops_epo.xml > ns_ops.html
+	${XSLTPROC} --stringparam current-date `date +%Y-%m-%d` html.xsl ns_ops_epo.xml > ns_ops.html
 
 txt: ns_ops_epo.xml
 	${XSLTPROC} text.xsl ns_ops_epo.xml
 
 cef: ns_ops_epo.xml
 	for cln in 1 2 3 4 ; do \
-		${XSLTPROC} --param clusterno $$cln caveatscef.xsl ns_ops_epo.xml > C$${cln}_CQ_EFW_INST_V00.cef ; \
+		${XSLTPROC} --param clusterno $$cln caveatscef.xsl ns_ops_epo.xml > C$${cln}_CQ_EFW_INST__20010128_V02.cef ; \
 	done
 
 ns_ops_epo.xml: ns_ops.xml
 	${XSLTPROC} addepoch.xsl ns_ops.xml > ns_ops_epo.xml
 
 clean:
-	rm -f ns_ops.html ns_ops_epo.xml ns_ops_c[1-4].dat C?_CQ_EFW_INST_V00.cef
+	rm -f ns_ops.html ns_ops_epo.xml ns_ops_c[1-4].dat C[1-4]_CQ_EFW_INST__20010128_V[0-9][0-9].cef
 
 test: test_epoch.xml test_epoch.xsl
 	echo "Tesing iso2epoch..."

mission/cluster/caa/caa-control/caveatscef.xsl

@@ -12,7 +12,7 @@ Valid parameter clusterno: values 1-4
 
 Uses exslt date & time and dynamic functions. Works with xsltproc.
 
-Copyright 2011-15 Jan Karlsson
+Copyright (c) 2011-23 Jan Karlsson
 
 Updated to exclude infinity (-1) stop time items
 
@@ -24,7 +24,7 @@ $Id$
   <xsl:text> </xsl:text>
   <xsl:value-of select="substring(date:time(),1,8)"/>
 !--------------------------------------------------------|
-FILE_NAME = "C<xsl:value-of select="$clusterno"/>_CQ_EFW_INST_V00.cef"
+FILE_NAME = "C<xsl:value-of select="$clusterno"/>_CQ_EFW_INST__20010128_V02.cef"
 FILE_FORMAT_VERSION = "CEF-2.0"
 END_OF_RECORD_MARKER = "$"
 include = "CL_CH_MISSION.ceh"
@@ -39,21 +39,21 @@ START_META     =   DATASET_VERSION
    ENTRY       =   "3"
 END_META       =   DATASET_VERSION
 START_META     =   LOGICAL_FILE_ID
-   ENTRY       =   "C<xsl:value-of select="$clusterno"/>_CQ_EFW_INST_V00"
+   ENTRY       =   "C<xsl:value-of select="$clusterno"/>_CQ_EFW_INST__20010128_V02"
 END_META       =   LOGICAL_FILE_ID
 START_META     =   VERSION_NUMBER
-   ENTRY       =   "00"
+   ENTRY       =   02
 END_META       =   VERSION_NUMBER
 START_META     =   FILE_TIME_SPAN
    VALUE_TYPE  =   ISO_TIME_RANGE
-   ENTRY       =   2001-02-01T00:00:00Z/2020-01-01T00:00:00Z
+   ENTRY       =   2001-01-28T00:00:00Z/2022-01-01T00:00:00Z
 END_META       =   FILE_TIME_SPAN
 START_META     =   GENERATION_DATE
    VALUE_TYPE  =   ISO_TIME
    ENTRY       =   <xsl:value-of select="substring(date:date-time(),1,19)"/>Z
 END_META       =   GENERATION_DATE
 START_META     =   FILE_CAVEATS
-   ENTRY       =   "Cluster <xsl:value-of select="$clusterno"/>. TBD stop time: 2020-01-01T00:00:00Z"
+   ENTRY       =   "Cluster <xsl:value-of select="$clusterno"/>. TBD stop time: 2022-01-01T00:00:00Z"
 END_META       =   FILE_CAVEATS
 !
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@@ -79,8 +79,8 @@ DATA_UNTIL = "END_OF_DATA"
 		<xsl:variable name="dt" select="@dt"/>
 		<xsl:if test="$dt != -1">
 			<xsl:value-of select="@start"/>/<xsl:choose>
-			<!--	<xsl:when test="$dt = -1">2020-01-01T00:00:00Z</xsl:when>        Infinity removed -->
-				<xsl:when test="$dt = -157">2020-01-01T00:00:00Z</xsl:when> <!-- TBD -->
+			<!--	<xsl:when test="$dt = -1">2025-01-01T00:00:00Z</xsl:when>        Infinity removed -->
+				<xsl:when test="$dt = -157">2022-01-01T00:00:00Z</xsl:when> <!-- TBD -->
 				<xsl:otherwise><xsl:value-of select="date:add(@start,concat('PT',$dt,'S'))"/></xsl:otherwise>
 			</xsl:choose>,"<xsl:value-of select="@sdesc"/>","<xsl:apply-templates select="@plan"/>","<xsl:value-of select="translate(translate(child::desc,'&#x9;&#xa;',''),'&#x22;',&quot;&#x27;&quot;)"/>" $
 </xsl:if> <!-- Not indented to not f**k up result file -->

mission/cluster/caa/caa-control/html.xsl

@@ -21,7 +21,7 @@ $Id$
 	</HEAD>
 	<BODY>
 	<H1 ALIGN="center">
-		Non-Standard Operations
+		EFW Non-Standard Operations Created (branch devel): <xsl:value-of select="$current-date"/>
 	</H1>
 	<H2>
 		<xsl:value-of select="//description"/>

mission/cluster/caa/caa-control/ns_ops_c1.dat

@@ -34,7 +34,7 @@
 1013799300 604800 1 12
 1013982300 1500 1 261
 1014187380 2100 1 261
-1014392580 -157 1 261
+1014392580 2400 1 261
 1021175637 1800 1 261
 1028658000 10800 0 1
 1032571080 11340 0 1

mission/cluster/caa/caa-control/ns_ops_c2.dat

@@ -28,7 +28,7 @@
 1010749500 230 1 2
 1013982300 1500 1 261
 1014187380 2100 1 261
-1014392580 -157 1 261
+1014392580 2400 1 261
 1016618340 85440 1 0
 1021175637 1800 1 261
 1028643000 1200 1 1
@@ -39,8 +39,8 @@
 1033574400 34200 1 9999
 1033785000 23400 1 9999
 1034017200 300 1 2
-1035774000 -157 1 261
-1035896400 -157 1 261
+1035774000 240 1 261
+1035896400 240 1 261
 1036484820 20 0 1
 1036484840 820 0 2
 1037145384 40 0 13
@@ -58,7 +58,6 @@
 1044304200 115500 1 134
 1045047720 10740 0 0
 1046073060 14400 0 1
-1047542160 -157 0 999
 1048087896 32258 0 0
 1048546887 85221 0 11
 1048741920 14400 0 1

mission/cluster/caa/caa-control/ns_ops_c3.dat

@@ -18,7 +18,7 @@
 1013982300 1500 1 261
 1013983200 120 1 261
 1014187380 2100 1 261
-1014392580 -157 1 261
+1014392580 2400 1 261
 1018947600 240 1 2
 1020074100 772560 0 1
 1020846660 2280 1 0
@@ -47,7 +47,7 @@
 1042653600 300 1 2
 1043309587 65644 0 0
 1043412636 3606 0 999
-1044098046 -157 0 999
+1044098046 294 0 999
 1045047720 10740 0 0
 1047079856 1200 1 261
 1047628394 3 0 0

mission/cluster/caa/caa-control/ns_ops_c4.dat

@@ -14,7 +14,7 @@
 1010770221 8 1 2
 1013982300 1500 1 261
 1014187380 2100 1 261
-1014392580 -157 1 261
+1014392580 2400 1 261
 1018962000 240 1 2
 1021175637 1800 1 261
 1024066924 2 0 1
@@ -31,15 +31,15 @@
 1033785000 23400 1 9999
 1034020800 300 1 2
 1035120112 75345 0 0
-1035774000 -157 1 261
-1035896400 -157 1 261
+1035774000 240 1 261
+1035896400 240 1 261
 1038499800 16200 0 0
 1039572126 2 0 1
 1040056320 45960 0 261
 1040501112 12474 1 261
 1040738700 16200 0 0
 1042635600 300 1 2
-1043434440 -157 0 0
+1043434440 71280 0 0
 1044216000 85320 1 134
 1044304200 115500 1 134
 1045047720 10740 0 0

mission/cluster/caa/caa_download.m

@@ -473,7 +473,14 @@
   end
   urlListDatasets = csa_parse_url(urlListDatasets);
   irf.log('warning',['Patience! Requesting "' dataset '" ' urlListDatasets]);
-  caalog=urlread(urlListDatasets); %#ok<URLRD> webread introduced in R2014b
+  if verLessThan('matlab', '8.4') % 8.4 = R2014b
+    caalog=urlread(urlListDatasets); %#ok<URLRD> webread introduced in R2014b
+  else
+    options = weboptions;
+    options.Timeout = 50; % seconds, default "5" is too short
+    options.ContentType = 'text'; % plaintext, don't have Matlab automatically decode it
+    caalog=webread(urlListDatasets, options);
+  end
   if isempty(caalog) % return empty output
     downloadStatus = [];
     return
@@ -500,7 +507,14 @@
   urlListDatasets = csa_parse_url(urlListDatasets);
   irf.log('warning','Patience! Requesting list of files.');
   irf.log('notice',['URL: ' urlListDatasets]);
-  caalist=urlread(urlListDatasets); %#ok<URLRD> webread introduced in R2014b
+  if verLessThan('matlab', '8.4') % 8.4 = R2014b
+    caalist=urlread(urlListDatasets); %#ok<URLRD> webread introduced in R2014b
+  else
+    options = weboptions;
+    options.Timeout = 50; % seconds, default 5 is too short
+    options.ContentType = 'text'; % plaintext, don't have Matlab automatically decode it
+    caalist=webread(urlListDatasets, options);
+  end
   irf.log('debug',['returned: ' caalist]);
   if isempty(caalist) % no datasets available
     irf.log('warning','There are no data sets available!');

mission/cluster/caa/ceh/CL_CH_EFW_EXP.ceh

@@ -31,7 +31,8 @@ END_META       =   INVESTIGATOR_COORDINATES
 ! List of standard reference documents for the experiment
 !
 START_META     =   EXPERIMENT_REFERENCES
-   ENTRY       =   "http://www.cluster.irfu.se/"
+   ENTRY       =   "https://doi.org/10.5270/esa-rp1zebe"
+   ENTRY       =   "https://cluster.irfu.se"
 END_META       =   EXPERIMENT_REFERENCES
 !
 ! Name, role and coordinates of experiment key personnel
@@ -51,16 +52,16 @@ START_META     =   EXPERIMENT_CAVEATS
    ENTRY       =   "Caveats for the Cluster EFW experiment:"
    ENTRY       =   ""
    ENTRY       =   "For general information on EFW, please visit the EFW home page"
-   ENTRY       =   "http://www.cluster.irfu.se"
+   ENTRY       =   "https://cluster.irfu.se"
    ENTRY       =   ""
    ENTRY       =   "For general information on EFW operations, both standard operations and"
    ENTRY       =   "anomalies, please visit the EFW operations home page"
-   ENTRY       =   "http://www.cluster.irfu.se/efw/ops"
+   ENTRY       =   "https://cluster.irfu.se/efw/ops"
    ENTRY       =   ""
    ENTRY       =   "For a chronological table of all non-standard operations and known"
    ENTRY       =   "instrument anomalies, please visit the EFW non-standard operations home"
    ENTRY       =   "page"
-   ENTRY       =   "http://www.cluster.irfu.se/efw/ops/ns_ops.html"
+   ENTRY       =   "https://cluster.irfu.se/efw/ops/ns_ops.html"
    ENTRY       =   ""
    ENTRY       =   "For more information on data quality and how the CAA data are processed"
    ENTRY       =   "please consult the EFW CAA Users Guide and the EFW CAA Interface Control"
@@ -76,16 +77,4 @@ END_META       =   INSTRUMENT_TYPE
 START_META     =   MEASUREMENT_TYPE
    ENTRY       =   "Electric_Field"
 END_META       =   MEASUREMENT_TYPE
-!
-! Name of dataset contact
-!
-START_META     =   CONTACT_COORDINATES
-   ENTRY       =   "Mats Andre>PI>[email protected]"
-END_META       =   CONTACT_COORDINATES
-!
-START_META     =   ACKNOWLEDGEMENT
-   ENTRY       =   "Please acknowledge the EFW team and ESA CAA in any"
-   ENTRY       =   "publication based upon use of these data"
-END_META       =   ACKNOWLEDGEMENT
-
 

mission/cluster/caa/ceh/CX_CQ_EFW_INST.ceh

@@ -11,13 +11,23 @@ END_META = DATA_TYPE
 START_META = DATASET_TITLE
 	ENTRY = "EFWXXX operations caveats"
 END_META = DATASET_TITLE
+START_META = DATASET_TYPE
+   ENTRY   = "Caveats"
+END_META   = DATASET_TYPE
 START_META = DATASET_DESCRIPTION
 	ENTRY = "This dataset contains operation caveats information"
 	ENTRY = "from the EFW experiment on the Cluster CXXX spacecraft"
 END_META = DATASET_DESCRIPTION 
 START_META = PROCESSING_LEVEL
 	ENTRY = "Auxiliary"
 END_META = PROCESSING_LEVEL
+START_META = CONTACT_COORDINATES
+   ENTRY   = "Mats Andre>PI>[email protected]"
+END_META   = CONTACT_COORDINATES
+START_META = ACKNOWLEDGEMENT
+   ENTRY   = "Please acknowledge the EFW team and the ESA Cluster Active Archive in any" 
+   ENTRY   = "publication based upon use of these data"
+END_META   = ACKNOWLEDGEMENT
 START_META = METADATA_TYPE
 	ENTRY = "CAA"
 END_META = METADATA_TYPE

mission/solar_orbiter/+solo/+adm/create_dataset_filename.m

@@ -163,25 +163,25 @@
 
 
 function s = create_time_interval_str(R)
-    function b = isfv(fnName, nComp)
+    function b = is_FV(fnName, nComp)
         b = isfield(R, fnName) && (numel(R.(fnName)) == nComp);
     end
 
     dv  = isfield(R, 'dateVec');
     dv1 = isfield(R, 'dateVec1');
     dv2 = isfield(R, 'dateVec2');
 
-    if     isfv('dateVec', 3) && ~dv1 && ~dv2
+    if     is_FV('dateVec', 3) && ~dv1 && ~dv2
         s = sprintf(...
             '%04i%02i%02i', ...
             R.dateVec);
 
-    elseif ~dv && isfv('dateVec1', 3) && isfv('dateVec2', 3)
+    elseif ~dv && is_FV('dateVec1', 3) && is_FV('dateVec2', 3)
         s = sprintf(...
             '%04i%02i%02i-%04i%02i%02i', ...
             R.dateVec1(:), R.dateVec2(:));
 
-    elseif ~dv && isfv('dateVec1', 6) && isfv('dateVec2', 6)
+    elseif ~dv && is_FV('dateVec1', 6) && is_FV('dateVec2', 6)
         s = sprintf(...
             '%04i%02i%02iT%02i%02i%02i-%04i%02i%02iT%02i%02i%02i', ...
             R.dateVec1(:), R.dateVec2(:));

mission/solar_orbiter/+solo/+sp/plot_LFR_CWF.m

@@ -140,7 +140,7 @@
         zvName = 'E';
     end
 
-    fillValue = getfillval(D, zvName);
+    fv = getfillval(D, zvName);
     zv = D.data.(zvName).data(:, i2);
-    zv = changem(zv, NaN, fillValue);
+    zv = changem(zv, NaN, fv);
 end

mission/solar_orbiter/+solo/+sp/plot_LFR_SWF.m

@@ -224,7 +224,7 @@
         zvName = 'E';
     end
 
-    fillValue = getfillval(D, zvName);
+    fv = getfillval(D, zvName);
     zv = D.data.(zvName).data(:, :, i3);
-    zv = changem(zv, NaN, fillValue);
+    zv = changem(zv, NaN, fv);
 end