From bb60a3b284796abfcdb990f0d1677f7286b38952 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rimbaud=20S=C3=A9bastien?=
 <sebastien.rimbaud@phelma.grenoble-inp.fr>
Date: Wed, 17 May 2017 11:36:49 +0200
Subject: [PATCH 1/5] Fix python 3.6 Type error in
 timefrequency.QSTFT.plotStokes and timefrequency.QSTFT.extractRidges

---
 bispy/.timefrequency.py.swp | Bin 0 -> 40960 bytes
 bispy/timefrequency.py      |  12 ++++++------
 2 files changed, 6 insertions(+), 6 deletions(-)
 create mode 100644 bispy/.timefrequency.py.swp

diff --git a/bispy/.timefrequency.py.swp b/bispy/.timefrequency.py.swp
new file mode 100644
index 0000000000000000000000000000000000000000..947c02ff9f70e54dca3d8f35017e4e0d0e6d66f1
GIT binary patch
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diff --git a/bispy/timefrequency.py b/bispy/timefrequency.py
index edfa612..31242c7 100644
--- a/bispy/timefrequency.py
+++ b/bispy/timefrequency.py
@@ -233,7 +233,7 @@ def extractRidges(self, parThresh=4, parMinD=3):
 
         # Extract ridges
         print('Extracting ridges')
-        self.ridges = _extractRidges(self.S0[:self.Nfft / 2, :], parThresh, parMinD)
+        self.ridges = _extractRidges(self.S0[:int(self.Nfft / 2), :], parThresh, parMinD)
 
 
     def plotStokes(self, cmocean=False):
@@ -259,10 +259,10 @@ def plotStokes(self, cmocean=False):
         N = np.size(self.t)
         fig, ax = plt.subplots(ncols=3, figsize=(12, 5), sharey=True)
 
-        im0 = ax[0].imshow(self.S1n[:self.Nfft / 2, :], origin='lower', interpolation='none', aspect='auto',cmap=cmap, extent=[self.t.min(), self.t.max(), 0, self.f[self.Nfft / 2-1]], vmin=-1, vmax=+1)
+        im0 = ax[0].imshow(self.S1n[:int(self.Nfft / 2), :], origin='lower', interpolation='none', aspect='auto',cmap=cmap, extent=[int(self.t.min()), int(self.t.max()), 0, self.f[int(self.Nfft / 2-1)]], vmin=-1, vmax=+1)
 
-        im1 = ax[1].imshow(self.S2n[:self.Nfft / 2, :], origin='lower', interpolation='none', aspect='auto',cmap=cmap, extent=[self.t.min(), self.t.max(), 0, self.f[self.Nfft / 2-1]], vmin=-1, vmax=+1)
-        im2 = ax[2].imshow(self.S3n[:self.Nfft / 2, :], origin='lower', interpolation='none', aspect='auto',cmap=cmap, extent=[self.t.min(), self.t.max(), 0, self.f[self.Nfft / 2-1]], vmin=-1, vmax=+1)
+        im1 = ax[1].imshow(self.S2n[:int(self.Nfft / 2), :], origin='lower', interpolation='none', aspect='auto',cmap=cmap, extent=[int(self.t.min()), int(self.t.max()), 0, self.f[int(self.Nfft / 2-1)]], vmin=-1, vmax=+1)
+        im2 = ax[2].imshow(self.S3n[:int(self.Nfft / 2), :], origin='lower', interpolation='none', aspect='auto',cmap=cmap, extent=[int(self.t.min()), int(self.t.max()), 0, self.f[int(self.Nfft / 2-1)]], vmin=-1, vmax=+1)
 
         # adjust figure
         fig.subplots_adjust(left=0.05, top=0.8, right=0.99, wspace=0.05)
@@ -340,10 +340,10 @@ def plotRidges(self, quivertdecim=10, cmocean=False):
 
         N = np.size(self.t)
         fig, ax = plt.subplots(ncols=3, figsize=(12, 5), sharey=True)
-        im0 = ax[0].imshow(self.S0[:self.Nfft / 2, :], interpolation='none', origin='lower', aspect='auto',cmap=cmap_S0, extent=[self.t.min(), self.t.max(), 0, self.f[self.Nfft / 2-1]])
+        im0 = ax[0].imshow(self.S0[:int(self.Nfft / 2), :], interpolation='none', origin='lower', aspect='auto',cmap=cmap_S0, extent=[int(self.t.min()), int(self.t.max()), 0, self.f[int(self.Nfft / 2-1)]])
 
 
-        im1 = ax[1].quiver(self.t[::self.spacing][::quivertdecim], self.f[:self.Nfft / 2], np.real(ori[:self.Nfft / 2, ::quivertdecim]), (np.imag(ori[:self.Nfft / 2, ::quivertdecim])), theta[:self.Nfft / 2, ::quivertdecim], clim=[-np.pi/2, np.pi/2], cmap=cmap_theta, headaxislength=0,headlength=0.001, pivot='middle',width=0.005, scale=15)
+        im1 = ax[1].quiver(self.t[::int(self.spacing)][::quivertdecim], self.f[:int(self.Nfft / 2)], np.real(ori[:int(self.Nfft / 2), ::quivertdecim]), (np.imag(ori[:int(self.Nfft / 2), ::quivertdecim])), theta[:int(self.Nfft / 2), ::quivertdecim], clim=[-np.pi/2, np.pi/2], cmap=cmap_theta, headaxislength=0,headlength=0.001, pivot='middle',width=0.005, scale=15)
 
         for r in self.ridges:
             points = np.array([self.t[::self.spacing][r[1]], self.f[r[0]]]).T.reshape(-1, 1, 2)

From 349222c26eb2b2009ca112353559010717466319 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rimbaud=20S=C3=A9bastien?=
 <sebastien.rimbaud@phelma.grenoble-inp.fr>
Date: Wed, 17 May 2017 11:46:46 +0200
Subject: [PATCH 2/5] Updating .gitignore for vim text editor

---
 .gitignore | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.gitignore b/.gitignore
index fd20fdd..7aee8be 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,9 @@
 
 *.pyc
+
+# Vim ignoring swap files
+
+*~
+*.swp
+*.swo
+

From 96322a817b369af9fbb4bed71ae50ccd08b09bea Mon Sep 17 00:00:00 2001
From: SRimbaud <sebastien.rimbaud@phelma.grenoble-inp.fr>
Date: Wed, 17 May 2017 11:59:40 +0200
Subject: [PATCH 3/5] Delete .timefrequency.py.swp

Vim temporary file, no need.
---
 bispy/.timefrequency.py.swp | Bin 40960 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 bispy/.timefrequency.py.swp

diff --git a/bispy/.timefrequency.py.swp b/bispy/.timefrequency.py.swp
deleted file mode 100644
index 947c02ff9f70e54dca3d8f35017e4e0d0e6d66f1..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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From bd6b173a1f993fd199fcdc8a9378564988ba2ff8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rimbaud=20S=C3=A9bastien?=
 <sebastien.rimbaud@phelma.grenoble-inp.fr>
Date: Thu, 18 May 2017 10:24:52 +0200
Subject: [PATCH 4/5] Correction bug in utils.py line 303 Stokes2geo return 4
 param not 3, phi added to get phi return param

---
 bispy/timefrequency.py | 2 ++
 bispy/utils.py         | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/bispy/timefrequency.py b/bispy/timefrequency.py
index 31242c7..befcea8 100644
--- a/bispy/timefrequency.py
+++ b/bispy/timefrequency.py
@@ -371,6 +371,7 @@ def plotRidges(self, quivertdecim=10, cmocean=False):
         cbar1.ax.xaxis.set_ticks_position('top')
 
         cbarax2 = fig.add_axes([0.686, 0.83, 0.303, 0.03])
+        print("-----Bug line im2-----\n{0}".format(im2))
         cbar2 = fig.colorbar(im2, cax=cbarax2, ticks=[-np.pi/4, 0, np.pi/4], orientation='horizontal')
         cbar2.ax.set_xticklabels([r'$-\frac{\pi}{4}$', r'$0$', r'$\frac{\pi}{4}$'])
         cbar2.ax.xaxis.set_ticks_position('top')
@@ -736,6 +737,7 @@ def _extractRidges(density, parThresh, parMinD):
 
         freqMask, timeMask = np.where(locMax)
 
+        FLAG = False #Avoid undifined FLAG if condition is false.
         if len(timeMask) > 1:
             FLAG = True
         while FLAG:
diff --git a/bispy/utils.py b/bispy/utils.py
index b698161..62ff5d8 100644
--- a/bispy/utils.py
+++ b/bispy/utils.py
@@ -300,7 +300,7 @@ def quat2euler(q):
     S2 = qqj_float[..., 1]
     S3 = - qqj_float[..., 3]
 
-    a, theta, chi = Stokes2geo(S0, S1, S2, S3)
+    a, theta, chi, phi = Stokes2geo(S0, S1, S2, S3)
 
     qi = quaternion.x
     qk = quaternion.z

From 1dac60eb7ef188421120f7329696fe745ddf84df Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rimbaud=20S=C3=A9bastien?=
 <sebastien.rimbaud@phelma.grenoble-inp.fr>
Date: Thu, 18 May 2017 10:34:43 +0200
Subject: [PATCH 5/5] Changing int by int division //

---
 bispy/timefrequency.py | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/bispy/timefrequency.py b/bispy/timefrequency.py
index befcea8..3191598 100644
--- a/bispy/timefrequency.py
+++ b/bispy/timefrequency.py
@@ -233,7 +233,7 @@ def extractRidges(self, parThresh=4, parMinD=3):
 
         # Extract ridges
         print('Extracting ridges')
-        self.ridges = _extractRidges(self.S0[:int(self.Nfft / 2), :], parThresh, parMinD)
+        self.ridges = _extractRidges(self.S0[:self.Nfft // 2, :], parThresh, parMinD)
 
 
     def plotStokes(self, cmocean=False):
@@ -259,10 +259,10 @@ def plotStokes(self, cmocean=False):
         N = np.size(self.t)
         fig, ax = plt.subplots(ncols=3, figsize=(12, 5), sharey=True)
 
-        im0 = ax[0].imshow(self.S1n[:int(self.Nfft / 2), :], origin='lower', interpolation='none', aspect='auto',cmap=cmap, extent=[int(self.t.min()), int(self.t.max()), 0, self.f[int(self.Nfft / 2-1)]], vmin=-1, vmax=+1)
+        im0 = ax[0].imshow(self.S1n[:self.Nfft // 2, :], origin='lower', interpolation='none', aspect='auto',cmap=cmap, extent=[int(self.t.min()), int(self.t.max()), 0, self.f[self.Nfft // 2-1]], vmin=-1, vmax=+1)
 
-        im1 = ax[1].imshow(self.S2n[:int(self.Nfft / 2), :], origin='lower', interpolation='none', aspect='auto',cmap=cmap, extent=[int(self.t.min()), int(self.t.max()), 0, self.f[int(self.Nfft / 2-1)]], vmin=-1, vmax=+1)
-        im2 = ax[2].imshow(self.S3n[:int(self.Nfft / 2), :], origin='lower', interpolation='none', aspect='auto',cmap=cmap, extent=[int(self.t.min()), int(self.t.max()), 0, self.f[int(self.Nfft / 2-1)]], vmin=-1, vmax=+1)
+        im1 = ax[1].imshow(self.S2n[:self.Nfft // 2, :], origin='lower', interpolation='none', aspect='auto',cmap=cmap, extent=[int(self.t.min()), int(self.t.max()), 0, self.f[self.Nfft // 2-1]], vmin=-1, vmax=+1)
+        im2 = ax[2].imshow(self.S3n[:self.Nfft // 2, :], origin='lower', interpolation='none', aspect='auto',cmap=cmap, extent=[int(self.t.min()), int(self.t.max()), 0, self.f[self.Nfft // 2-1]], vmin=-1, vmax=+1)
 
         # adjust figure
         fig.subplots_adjust(left=0.05, top=0.8, right=0.99, wspace=0.05)
@@ -340,10 +340,10 @@ def plotRidges(self, quivertdecim=10, cmocean=False):
 
         N = np.size(self.t)
         fig, ax = plt.subplots(ncols=3, figsize=(12, 5), sharey=True)
-        im0 = ax[0].imshow(self.S0[:int(self.Nfft / 2), :], interpolation='none', origin='lower', aspect='auto',cmap=cmap_S0, extent=[int(self.t.min()), int(self.t.max()), 0, self.f[int(self.Nfft / 2-1)]])
+        im0 = ax[0].imshow(self.S0[:self.Nfft // 2, :], interpolation='none', origin='lower', aspect='auto',cmap=cmap_S0, extent=[int(self.t.min()), int(self.t.max()), 0, self.f[self.Nfft // 2-1]])
 
 
-        im1 = ax[1].quiver(self.t[::int(self.spacing)][::quivertdecim], self.f[:int(self.Nfft / 2)], np.real(ori[:int(self.Nfft / 2), ::quivertdecim]), (np.imag(ori[:int(self.Nfft / 2), ::quivertdecim])), theta[:int(self.Nfft / 2), ::quivertdecim], clim=[-np.pi/2, np.pi/2], cmap=cmap_theta, headaxislength=0,headlength=0.001, pivot='middle',width=0.005, scale=15)
+        im1 = ax[1].quiver(self.t[::int(self.spacing)][::quivertdecim], self.f[:int(self.Nfft / 2)], np.real(ori[:self.Nfft // 2, ::quivertdecim]), (np.imag(ori[:self.Nfft // 2, ::quivertdecim])), theta[:self.Nfft // 2, ::quivertdecim], clim=[-np.pi/2, np.pi/2], cmap=cmap_theta, headaxislength=0,headlength=0.001, pivot='middle',width=0.005, scale=15)
 
         for r in self.ridges:
             points = np.array([self.t[::self.spacing][r[1]], self.f[r[0]]]).T.reshape(-1, 1, 2)
@@ -371,7 +371,6 @@ def plotRidges(self, quivertdecim=10, cmocean=False):
         cbar1.ax.xaxis.set_ticks_position('top')
 
         cbarax2 = fig.add_axes([0.686, 0.83, 0.303, 0.03])
-        print("-----Bug line im2-----\n{0}".format(im2))
         cbar2 = fig.colorbar(im2, cax=cbarax2, ticks=[-np.pi/4, 0, np.pi/4], orientation='horizontal')
         cbar2.ax.set_xticklabels([r'$-\frac{\pi}{4}$', r'$0$', r'$\frac{\pi}{4}$'])
         cbar2.ax.xaxis.set_ticks_position('top')
@@ -384,7 +383,7 @@ def plotRidges(self, quivertdecim=10, cmocean=False):
         ax[0].set_ylabel('Frequency [Hz]')
 
         ax[0].set_title('Time-Frequency energy density', y=1.14)
-        
+
         ax[1].set_title('Instantaneous orientation', y=1.14)
         ax[2].set_title('Instantaneous ellipticity', y=1.14)