From 6f56004e3f6f9f8630c6fb3bdfb0fed7479a6590 Mon Sep 17 00:00:00 2001
From: Jan Caron <j.caron@fz-juelich.de>
Date: Tue, 17 Mar 2020 08:31:19 +0100
Subject: [PATCH] Fixed xy ordering error in plot_holo (np.gradient)
---
pyramid/phasemap.py | 7 ++++---
pyramid/version.py | 2 +-
src/empyre/version.py | 4 ++++
3 files changed, 9 insertions(+), 4 deletions(-)
create mode 100644 src/empyre/version.py
diff --git a/pyramid/phasemap.py b/pyramid/phasemap.py
index c3b847d..9a32643 100644
--- a/pyramid/phasemap.py
+++ b/pyramid/phasemap.py
@@ -770,8 +770,9 @@ class PhaseMap(object):
holo /= 2 # Rescale to [0, 1]
# Calculate the phase gradients:
# B = rot(A) --> B_x = grad_y(A_z), B_y = -grad_x(A_z); phi_m ~ -int(A_z)
- # sign switch --> B_x = -grad_y(phi_m), B_y = grad_x(phi_m)
- grad_x, grad_y = np.gradient(self.phase, self.a, self.a)
+ # for projection along +z: sign switch --> B_x = -grad_y(phi_m), B_y = grad_x(phi_m)
+ # for projection along -z: NO sign switch --> B_x = grad_y(phi_m), B_y = -grad_x(phi_m)
+ grad_y, grad_x = np.gradient(self.phase, self.a, self.a)
# Clip outliers:
outlier_x = np.abs(grad_x - np.mean(grad_x)) < sigma_clip * np.std(grad_x)
grad_x_sigma = np.where(outlier_x, grad_x, np.nan)
@@ -784,7 +785,7 @@ class PhaseMap(object):
# Calculate colors:
if cmap is None:
cmap = colors.CMAP_CIRCULAR_DEFAULT
- vector = np.asarray((grad_x, -grad_y, np.zeros_like(grad_x)))
+ vector = np.asarray((grad_y, -grad_x, np.zeros_like(grad_x)))
rgb = cmap.rgb_from_vector(vector)
rgb = (holo.T * rgb.T).T.astype(np.uint8)
holo_image = Image.fromarray(rgb)
diff --git a/pyramid/version.py b/pyramid/version.py
index db94eca..a2c91c2 100644
--- a/pyramid/version.py
+++ b/pyramid/version.py
@@ -1,4 +1,4 @@
# -*- coding: utf-8 -*-
""""This file was automatically generated by `setup.py`"""
version = "0.1.0.dev0"
-git_revision = "a9c22581a4bfd12bfadd9001ccf893f77fc1a6de"
+git_revision = "a44d6c228b1c4dbf867bc2982f28d1cfd9a0c249"
diff --git a/src/empyre/version.py b/src/empyre/version.py
new file mode 100644
index 0000000..cff0ebc
--- /dev/null
+++ b/src/empyre/version.py
@@ -0,0 +1,4 @@
+# -*- coding: utf-8 -*-
+""""This file was automatically generated by `setup.py`"""
+version = "0.0.0"
+git_revision = "ec897efbbcdfe4a72ae8f70f82072e03b521bb26"
--
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