From 745531333975dbd6be79b7db162da6e39dc4c616 Mon Sep 17 00:00:00 2001
From: "borondics.accounts@gmail.com" <borondics@users.noreply.github.com>
Date: Wed, 18 Oct 2023 16:28:55 +0200
Subject: [PATCH 1/5] added icon to 2DCOS

---
 .../spectroscopy/widgets/icons/2dcos.svg      | 88 +++++++++++++++++++
 1 file changed, 88 insertions(+)
 create mode 100644 orangecontrib/spectroscopy/widgets/icons/2dcos.svg

diff --git a/orangecontrib/spectroscopy/widgets/icons/2dcos.svg b/orangecontrib/spectroscopy/widgets/icons/2dcos.svg
new file mode 100644
index 000000000..11c6e9970
--- /dev/null
+++ b/orangecontrib/spectroscopy/widgets/icons/2dcos.svg
@@ -0,0 +1,88 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+   width="48mm"
+   height="48mm"
+   viewBox="0 0 48 48"
+   version="1.1"
+   id="svg1"
+   inkscape:version="1.3 (0e150ed, 2023-07-21)"
+   sodipodi:docname="2dcos.svg"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:xlink="http://www.w3.org/1999/xlink"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:svg="http://www.w3.org/2000/svg">
+  <sodipodi:namedview
+     id="namedview1"
+     pagecolor="#ffffff"
+     bordercolor="#999999"
+     borderopacity="1"
+     inkscape:showpageshadow="0"
+     inkscape:pageopacity="0"
+     inkscape:pagecheckerboard="0"
+     inkscape:deskcolor="#d1d1d1"
+     inkscape:document-units="mm"
+     inkscape:zoom="3.2144363"
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+     inkscape:cy="80.262908"
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+     inkscape:window-height="847"
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+     inkscape:window-y="25"
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+     inkscape:current-layer="layer1" />
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From 0e4bddb8dc0394b2f1fd9007f6ab7866d84fb448 Mon Sep 17 00:00:00 2001
From: "borondics.accounts@gmail.com" <borondics@users.noreply.github.com>
Date: Wed, 18 Oct 2023 16:48:54 +0200
Subject: [PATCH 2/5] changed the code to load icon

---
 orangecontrib/spectroscopy/widgets/owcos.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/orangecontrib/spectroscopy/widgets/owcos.py b/orangecontrib/spectroscopy/widgets/owcos.py
index d9f07c475..46cda8929 100644
--- a/orangecontrib/spectroscopy/widgets/owcos.py
+++ b/orangecontrib/spectroscopy/widgets/owcos.py
@@ -182,8 +182,7 @@ class OWCos(OWWidget):
     description = (
         "Perform 2D correlation analysis with series spectra")
 
-    # TODO - needs icon
-    icon = "icons/average.svg"
+    icon = "icons/2dcos.svg"
 
     graph_name = "plotview"  # need this to show the save button
 
@@ -444,7 +443,8 @@ def plotCOS(self):
                                     (topSPwn.max() - topSPwn.min()),
                                     (leftSPwn.max() - leftSPwn.min())))
 
-            self.cbarCOS.set_range(-1 * np.absolute(cosmat).max(), np.absolute(cosmat).max())
+            print(np.nanmax(np.absolute(cosmat)), np.nanmax(np.absolute(cosmat)))
+            self.cbarCOS.set_range(-1 * np.nanmax(np.absolute(cosmat)), np.nanmax(np.absolute(cosmat)))
             self.cbarCOS.set_colors(np.array(colorcet.diverging_bwr_40_95_c42) * 255)
 
             for s in leftSP:
@@ -487,4 +487,4 @@ def commit(self):
     from Orange.widgets.utils.widgetpreview import WidgetPreview
 
     WidgetPreview(OWCos).run(set_data1=Orange.data.Table("collagen"), set_data2=None)
-    # WidgetPreview(OWCos).run(set_data1=Orange.data.Table("/Users/borondics/2dcos-test-lShift2b_large.dat"), set_data2=None)
\ No newline at end of file
+    # WidgetPreview(OWCos).run(set_data1=Orange.data.Table("/Users/borondics/2dcos-test-lShift2b_large.dat"), set_data2=None)

From 11b5119c31179f837721f43ec62990599d3a03c9 Mon Sep 17 00:00:00 2001
From: "borondics.accounts@gmail.com" <borondics@users.noreply.github.com>
Date: Thu, 19 Oct 2023 16:12:12 +0200
Subject: [PATCH 3/5] new icon for 2DCOS

---
 .../spectroscopy/widgets/icons/2dcos.svg      | 1281 ++++++++++++++++-
 1 file changed, 1233 insertions(+), 48 deletions(-)

diff --git a/orangecontrib/spectroscopy/widgets/icons/2dcos.svg b/orangecontrib/spectroscopy/widgets/icons/2dcos.svg
index 11c6e9970..b782dcc15 100644
--- a/orangecontrib/spectroscopy/widgets/icons/2dcos.svg
+++ b/orangecontrib/spectroscopy/widgets/icons/2dcos.svg
@@ -9,12 +9,11 @@
    id="svg1"
    inkscape:version="1.3 (0e150ed, 2023-07-21)"
    sodipodi:docname="2dcos.svg"
+   xml:space="preserve"
    xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
    xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
-   xmlns:xlink="http://www.w3.org/1999/xlink"
    xmlns="http://www.w3.org/2000/svg"
-   xmlns:svg="http://www.w3.org/2000/svg">
-  <sodipodi:namedview
+   xmlns:svg="http://www.w3.org/2000/svg"><sodipodi:namedview
      id="namedview1"
      pagecolor="#ffffff"
      bordercolor="#999999"
@@ -24,65 +23,1251 @@
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+     inkscape:zoom="1.0208232"
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From 1e34c2e4d851accc929b31a050c885b130b43db1 Mon Sep 17 00:00:00 2001
From: "borondics.accounts@gmail.com" <borondics@users.noreply.github.com>
Date: Thu, 19 Oct 2023 16:14:27 +0200
Subject: [PATCH 4/5] took out unnecessary line

---
 orangecontrib/spectroscopy/widgets/owcos.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/orangecontrib/spectroscopy/widgets/owcos.py b/orangecontrib/spectroscopy/widgets/owcos.py
index 46cda8929..8d02bd010 100644
--- a/orangecontrib/spectroscopy/widgets/owcos.py
+++ b/orangecontrib/spectroscopy/widgets/owcos.py
@@ -487,4 +487,3 @@ def commit(self):
     from Orange.widgets.utils.widgetpreview import WidgetPreview
 
     WidgetPreview(OWCos).run(set_data1=Orange.data.Table("collagen"), set_data2=None)
-    # WidgetPreview(OWCos).run(set_data1=Orange.data.Table("/Users/borondics/2dcos-test-lShift2b_large.dat"), set_data2=None)

From d1c22be156f3fe451a13db27efaf2b3d4cac779d Mon Sep 17 00:00:00 2001
From: "borondics.accounts@gmail.com" <borondics@users.noreply.github.com>
Date: Thu, 19 Oct 2023 16:18:00 +0200
Subject: [PATCH 5/5] removed print

---
 orangecontrib/spectroscopy/widgets/owcos.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/orangecontrib/spectroscopy/widgets/owcos.py b/orangecontrib/spectroscopy/widgets/owcos.py
index 8d02bd010..238ede988 100644
--- a/orangecontrib/spectroscopy/widgets/owcos.py
+++ b/orangecontrib/spectroscopy/widgets/owcos.py
@@ -443,7 +443,6 @@ def plotCOS(self):
                                     (topSPwn.max() - topSPwn.min()),
                                     (leftSPwn.max() - leftSPwn.min())))
 
-            print(np.nanmax(np.absolute(cosmat)), np.nanmax(np.absolute(cosmat)))
             self.cbarCOS.set_range(-1 * np.nanmax(np.absolute(cosmat)), np.nanmax(np.absolute(cosmat)))
             self.cbarCOS.set_colors(np.array(colorcet.diverging_bwr_40_95_c42) * 255)