From 7718120738c1a88fd88454c7993655248861461f Mon Sep 17 00:00:00 2001
From: Eric Prestat <eric.prestat@gmail.com>
Date: Thu, 24 Sep 2020 11:16:35 +0100
Subject: [PATCH 1/5] Keep hyperspy signal metadata.

---
 pguresvt/hspy.py | 14 +-------------
 1 file changed, 1 insertion(+), 13 deletions(-)

diff --git a/pguresvt/hspy.py b/pguresvt/hspy.py
index b9c1ebf..357b004 100644
--- a/pguresvt/hspy.py
+++ b/pguresvt/hspy.py
@@ -1,8 +1,6 @@
 # Author: Tom Furnival
 # License: GPLv3
 
-from hyperspy.signals import BaseSignal
-
 from .svt import SVT
 
 
@@ -52,16 +50,6 @@ def _prepare_to_denoise(self, signal):
                 f"Expected 1D or 2D signal - got dimension {sig_dim}"
             )
 
-    def _denoised_data_to_signal(self):
-        """Converts denoised data back to a HyperSpy signal."""
-        signal = BaseSignal(self.Y_)
-
-        if self._signal_type == "spectrum":
-            return signal.as_signal1D(2)
-
-        if self._signal_type == "image":
-            return signal.as_signal2D((1, 2))
-
     def denoise(self, signal):
         """Denoises an arbitrary HyperSpy signal.
 
@@ -80,4 +68,4 @@ def denoise(self, signal):
 
         super(HSPYSVT, self).denoise(self._X)
 
-        return self._denoised_data_to_signal()
+        return signal._deepcopy_with_new_data(self.Y_.T)

From f5d977102899deac467f26c259f8893e3bae5e85 Mon Sep 17 00:00:00 2001
From: Eric Prestat <eric.prestat@gmail.com>
Date: Thu, 24 Sep 2020 11:24:27 +0100
Subject: [PATCH 2/5] Add title to metadata.

---
 pguresvt/hspy.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/pguresvt/hspy.py b/pguresvt/hspy.py
index 357b004..5116e5d 100644
--- a/pguresvt/hspy.py
+++ b/pguresvt/hspy.py
@@ -68,4 +68,8 @@ def denoise(self, signal):
 
         super(HSPYSVT, self).denoise(self._X)
 
-        return signal._deepcopy_with_new_data(self.Y_.T)
+        denoised_signal = signal._deepcopy_with_new_data(self.Y_.T)
+        new_title = f"Denoised {signal.metadata.General.title}".strip()
+        denoised_signal.metadata.General.title = new_title
+
+        return denoised_signal

From 2a54cfeb2aad2059c75b0d8cc54c08c5fcc20caf Mon Sep 17 00:00:00 2001
From: Eric Prestat <eric.prestat@gmail.com>
Date: Thu, 24 Sep 2020 11:25:19 +0100
Subject: [PATCH 3/5] Fix example notebook (negative value error).

---
 examples/PGURE-SVT-HyperSpy-Demo.ipynb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/PGURE-SVT-HyperSpy-Demo.ipynb b/examples/PGURE-SVT-HyperSpy-Demo.ipynb
index 83a256d..9159838 100644
--- a/examples/PGURE-SVT-HyperSpy-Demo.ipynb
+++ b/examples/PGURE-SVT-HyperSpy-Demo.ipynb
@@ -78,7 +78,7 @@
    "source": [
     "random_state = 123\n",
     "detector_gain = 0.1\n",
-    "detector_offset = 0.1\n",
+    "detector_offset = 0.5\n",
     "detector_sigma = 0.1\n",
     "\n",
     "noisy_data = mixed_noise_model(\n",
@@ -228,7 +228,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.7.9"
   }
  },
  "nbformat": 4,

From 4a223eb74ed6ec1d21b89067cd258df36d28c284 Mon Sep 17 00:00:00 2001
From: Eric Prestat <eric.prestat@gmail.com>
Date: Thu, 24 Sep 2020 11:27:02 +0100
Subject: [PATCH 4/5] Remove optional openblas dependency to compile C
 extension.

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 676beb6..13b50c8 100644
--- a/setup.py
+++ b/setup.py
@@ -11,7 +11,7 @@
         "pguresvt._pguresvt",
         sources=["pguresvt/_pguresvt.pyx"],
         include_dirs=["pguresvt/", "src/", np.get_include()],
-        libraries=["openblas", "lapack", "armadillo", "nlopt"],
+        libraries=["lapack", "armadillo", "nlopt"],
         language="c++",
         extra_compile_args=[
             "-fPIC",

From 2150463e9a6aca2d201b8b98eea9e5bfeabde63b Mon Sep 17 00:00:00 2001
From: Eric Prestat <eric.prestat@gmail.com>
Date: Thu, 24 Sep 2020 13:54:03 +0100
Subject: [PATCH 5/5] Fix tranposition.

---
 pguresvt/hspy.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/pguresvt/hspy.py b/pguresvt/hspy.py
index 5116e5d..0587c3b 100644
--- a/pguresvt/hspy.py
+++ b/pguresvt/hspy.py
@@ -68,7 +68,12 @@ def denoise(self, signal):
 
         super(HSPYSVT, self).denoise(self._X)
 
-        denoised_signal = signal._deepcopy_with_new_data(self.Y_.T)
+        if self._signal_type == "spectrum":
+            axes = (1, 0)
+        elif self._signal_type == "image":
+            axes = (2, 0, 1)
+
+        denoised_signal = signal._deepcopy_with_new_data(self.Y_.transpose(axes))
         new_title = f"Denoised {signal.metadata.General.title}".strip()
         denoised_signal.metadata.General.title = new_title