From eed05fe3fe00f31baa503829857cbe0dd6105dd2 Mon Sep 17 00:00:00 2001
From: Oksana Zaharko <Oksana.Zaharko@psi.ch>
Date: Thu, 19 Mar 2020 12:05:45 +0100
Subject: [PATCH] OZ renamed zebra.py into h5.py, added reading angles

---
 pyzebra/h5.py   | 69 +++++++++++++++++++++++++++++++++++++++++++++++++
 pyzebra/xtal.py | 22 ++++++++++++++++
 2 files changed, 91 insertions(+)
 create mode 100644 pyzebra/h5.py
 create mode 100644 pyzebra/xtal.py

diff --git a/pyzebra/h5.py b/pyzebra/h5.py
new file mode 100644
index 0000000..be51205
--- /dev/null
+++ b/pyzebra/h5.py
@@ -0,0 +1,69 @@
+import h5py
+
+def read_h5meta(filepath):
+    """Read and parse content of a h5meta file.
+
+    Args:
+        filepath (str): File path of a h5meta file.
+
+    Returns:
+        dict: A dictionary with section names and their content.
+    """
+    h5meta_content = dict()
+    with open(filepath, "r") as h5meta_file:
+        line = h5meta_file.readline()
+        while line:
+            if line.startswith("#begin"):
+                # read section
+                section = line[7:-1]  # len("#begin ") = 7
+                h5meta_content[section] = []
+                line = h5meta_file.readline()
+                while not line.startswith("#end"):
+                    h5meta_content[section].append(line[:-1])
+                    line = h5meta_file.readline()
+
+            # read next line after section's end
+            line = h5meta_file.readline()
+
+    return h5meta_content
+
+
+def read_detector_data(filepath):
+    """Read detector data and angles from an h5 file.
+
+    Args:
+        filepath (str): File path of an h5 file.
+
+    Returns:
+        ndarray: A 3D array of data, rot_angle, pol_angle, tilt_angle.
+    """
+    with h5py.File(filepath, "r") as h5f:
+        detector_data = h5f["/entry1/area_detector2/data"][:]
+
+        # reshape data to a correct shape (2006 issue)
+        n, cols, rows = detector_data.shape
+        detector_data = detector_data.reshape(n, rows, cols)
+
+        rot_angle = h5f["/entry1/area_detector2/rotation_angle"][:]
+        pol_angle = h5f["/entry1/ZEBRA/area_detector2/polar_angle"][:]
+        tlt_angle = h5f["/entry1/ZEBRA/area_detector2/tilt_angle"][:]
+
+    return detector_data, pol_angle, rot_angle, tlt_angle
+
+def open_h5meta(filepath):
+    """Open h5meta file like *.cami
+
+    Args:
+        filepath (str): File path of a h5meta file.
+
+    Returns:
+        dict: A dictionary with h5 names and their detector data and angles.
+    """
+    data = dict()
+    angles = dict()
+    h5meta_content = read_h5meta(filepath)
+    for file in h5meta_content["filelist"]:
+        data[file] = read_detector_data(file)
+        angles[file]  = read_angle_data(file)
+
+    return data, angles
diff --git a/pyzebra/xtal.py b/pyzebra/xtal.py
new file mode 100644
index 0000000..f6e9db1
--- /dev/null
+++ b/pyzebra/xtal.py
@@ -0,0 +1,22 @@
+import  numpy as np
+
+def z4frgn(wave,ga,nu):
+    """CALCULATES DIFFRACTION VECTOR IN LAB SYSTEM FROM GA AND NU
+
+    Args:
+        WAVE,GA,NU
+
+    Returns:
+        Z4
+    """
+    sin = np.sin
+    cos = np.cos
+    pir = 180/np.pi
+    gar = ga/pir
+    nur = nu/pir
+    z4 = [0., 0., 0.]
+    z4[0]=( sin(gar)*cos(nur)    )/wave
+    z4[1]=( cos(gar)*cos(nur)-1. )/wave
+    z4[2]=( sin(nur)             )/wave
+
+    return z4