From 3e2bd8d182016859f7ba08fd87350ecdd0ddea2a Mon Sep 17 00:00:00 2001
From: Vesna Tanko <tankovesna@hotmail.com>
Date: Tue, 6 Nov 2018 10:36:27 +0100
Subject: [PATCH] OWFreeViz: Fix optimization for data with missing values

---
 Orange/widgets/visualize/owfreeviz.py            | 15 ++++++++-------
 Orange/widgets/visualize/tests/test_owfreeviz.py |  2 +-
 Orange/widgets/visualize/utils/widget.py         |  1 +
 3 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/Orange/widgets/visualize/owfreeviz.py b/Orange/widgets/visualize/owfreeviz.py
index c1f9583c4c5..2fe3cf1833b 100644
--- a/Orange/widgets/visualize/owfreeviz.py
+++ b/Orange/widgets/visualize/owfreeviz.py
@@ -353,12 +353,12 @@ def prepare_projection_data(self):
             self._X = self._Y = self.valid_data = None
             return
 
-        self._X = self.data.X.copy()
-        self._X -= np.nanmean(self._X, axis=0)
-        span = np.ptp(self._X[self.valid_data], axis=0)
+        self._X = self.data.X[self.valid_data]
+        self._X -= np.mean(self._X, axis=0)
+        span = np.ptp(self._X, axis=0)
         self._X[:, span > 0] /= span[span > 0].reshape(1, -1)
 
-        self._Y = self.data.Y
+        self._Y = self.data.Y[self.valid_data]
         if self.data.domain.class_var.is_discrete:
             self._Y = self._Y.astype(int)
 
@@ -370,9 +370,10 @@ def init_embedding_coords(self):
     def get_embedding(self):
         if self.data is None:
             return None
-        embedding = np.dot(self._X, self.projection)
-        embedding /= \
-            np.max(np.linalg.norm(embedding[self.valid_data], axis=1)) or 1
+        EX = np.dot(self._X, self.projection)
+        EX /= np.max(np.linalg.norm(EX, axis=1)) or 1
+        embedding = np.zeros((len(self.data), 2), dtype=np.float)
+        embedding[self.valid_data] = EX
         return embedding
 
     def get_anchors(self):
diff --git a/Orange/widgets/visualize/tests/test_owfreeviz.py b/Orange/widgets/visualize/tests/test_owfreeviz.py
index 0120a8c746c..988cf84b6ef 100644
--- a/Orange/widgets/visualize/tests/test_owfreeviz.py
+++ b/Orange/widgets/visualize/tests/test_owfreeviz.py
@@ -39,7 +39,7 @@ def test_error_msg(self):
         self.assertFalse(self.widget.Error.not_enough_class_vars.is_shown())
 
     def test_optimization(self):
-        self.send_signal(self.widget.Inputs.data, self.data)
+        self.send_signal(self.widget.Inputs.data, self.heart_disease)
         self.widget.btn_start.click()
 
     def test_optimization_cancelled(self):
diff --git a/Orange/widgets/visualize/utils/widget.py b/Orange/widgets/visualize/utils/widget.py
index 610f806926a..43c6eeb11c7 100644
--- a/Orange/widgets/visualize/utils/widget.py
+++ b/Orange/widgets/visualize/utils/widget.py
@@ -550,6 +550,7 @@ def clear(self):
         self.data = None
         self.valid_data = None
         self.selection = None
+        self.graph.selection = None
 
     def onDeleteWidget(self):
         super().onDeleteWidget()