Fixes #83 #84 #86

JaneliaSciComp · Feb 11, 2019 · b742df7 · b742df7
1 parent 643662c
commit b742df7
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Showing 7 changed files with 51 additions and 7 deletions.
diff --git a/+jrclust/+controllers/+curate/CurateController.m b/+jrclust/+controllers/+curate/CurateController.m
@@ -638,7 +638,7 @@ function addMenu(obj, hFig)
             hFig.figApply(@set, 'MenuBar','None');
 
             obj.hMenus('FileMenu') = hFig.uimenu('Label', 'File');
-            uimenu(obj.hMenus('FileMenu'), 'Label', 'Save', 'Callback', @obj.saveFiles);
+            uimenu(obj.hMenus('FileMenu'), 'Label', 'Save', 'Callback', @(hO, hE) obj.saveFiles());
             uimenu(obj.hMenus('FileMenu'), 'Label', 'Save figures as .fig', 'Callback', @(hO, hE) obj.saveFigures('.fig'));
             uimenu(obj.hMenus('FileMenu'), 'Label', 'Save figures as .png', 'Callback', @(hO, hE) obj.saveFigures('.png'));
             uimenu(obj.hMenus('FileMenu'), 'Label', 'Export units to csv', 'Callback', @(hO, hE) obj.hClust.exportToCSV(), 'Separator', 'on');

diff --git a/+jrclust/Config.m b/+jrclust/Config.m
@@ -316,7 +316,11 @@ function validateParams(obj)
                 obj.error('nSitesExcl is too large or nSiteDir is too small', 'Bad configuration');
             end
 
-            obj.ignoreSites = obj.ignoreSites(ismember(obj.ignoreSites, obj.siteMap));
+            % ignoreSites/ignoreChans
+            obj.ignoreChans = obj.ignoreChans(ismember(obj.ignoreChans, obj.siteMap));
+            obj.ignoreSites = intersect(obj.ignoreSites, 1:numel(obj.siteMap));
+            obj.ignoreSites = union(obj.ignoreSites, find(ismember(obj.siteMap, obj.ignoreChans)));
+
             obj.siteNeighbors = findSiteNeighbors(obj.siteLoc, 2*obj.nSiteDir + 1, obj.ignoreSites, obj.shankMap);
 
             % boost that gain

diff --git a/CHANGELOG.TXT b/CHANGELOG.TXT
@@ -1,3 +1,14 @@
+11 Feb 2019
+
+# Parameters
+- ignoreChans (formerly viChanZero) (re)implemented to address issue #83.
+
+# Config
+- canonical version of ignoreSites was computed wrong in validation; this has been fixed
+
+# CurateController
+- "File > Save" menu callback crashed with "Too many input arguments" (see #86); this has been fixed
+
 7 Feb 2019
 
 # Parameters

diff --git a/default.prm b/default.prm
@@ -23,7 +23,8 @@ blankThresh = []; % (formerly blank_thresh) Threshold (in MADs) above which to r
 filterType = 'ndiff'; % (formerly vcFilter) Type of filter to use on raw data
 filtOrder = 3; % Bandpass filter order
 freqLimBP = [300, 3000]; % (formerly freqLim) Frequency cutoffs for bandpass filter
-ignoreSites = []; % (formerly viSiteZero) Sites to ignore manually
+ignoreChans = []; % (formerly viChanZero) Channel numbers to ignore manually
+ignoreSites = []; % (formerly viSiteZero) Site IDs to ignore manually
 
 % SPIKE DETECTION PARAMETERS
 blankPeriod = 5; % (formerly blank_period_ms) Duration of blanking period (in ms) when the common mean exceeds blankThresh

diff --git a/docs/parameters/index.rst b/docs/parameters/index.rst
@@ -238,14 +238,28 @@ JRCLUST will skip this many bytes at the beginning of your recording file.
 
 **Default** is 0.
 
+.. _ignoreChans:
+
+ignoreChans
+^^^^^^^^^^^
+
+(Formerly ``viChanZero``)
+
+Channel numbers to ignore manually.
+Should be an array of integers between 1 and nChans.
+These values will be merged into :ref:`ignoreSites`.
+
+**Default** is empty.
+
 .. _ignoreSites:
 
 ignoreSites
 ^^^^^^^^^^^
 
 (Formerly ``viSiteZero``)
 
-Sites to ignore manually.
+Site IDs to ignore manually.
+Should be an array of integers between 1 and nSites.
 
 **Default** is empty.
 

diff --git a/jrc.json b/jrc.json
@@ -4,10 +4,10 @@
         "major": 4,
         "minor": 0,
         "release": 0,
-        "tag": "alpha-patch2",
+        "tag": "alpha-patch4",
         "codename": "Edward"
     },
-    "changeDate": "7 Feb 2019",
+    "changeDate": "11 Feb 2019",
     "authors": [
         "James Jun"
     ],

diff --git a/params.json b/params.json
@@ -243,8 +243,21 @@
             },
             "section": ["recording file"]
         },
+        "ignoreChans": {
+            "description": "Channel numbers to ignore manually",
+            "comment": "",
+            "default_value": [],
+            "validation": {
+                "classes": ["numeric"],
+                "attributes": [
+                    "integer",
+                    "positive"
+                ]
+            },
+            "section": ["preprocessing"]
+        },
         "ignoreSites": {
-            "description": "Sites to ignore manually",
+            "description": "Site IDs to ignore manually",
             "comment": "",
             "default_value": [],
             "validation": {
@@ -1764,6 +1777,7 @@
         "vcFilter": "filterType",
         "vcFilter_show": "dispFilter",
         "vcLabel_aux": "auxLabel",
+        "viChanZero": "ignoreChans",
         "viShank_site": "shankMap",
         "viSite2Chan": "siteMap",
         "viSiteZero": "ignoreSites",