From cf6527af131dc2fc02f0b8845ae4356d1c3f0a69 Mon Sep 17 00:00:00 2001
From: Ivan Usov <ivan.usov@psi.ch>
Date: Tue, 29 Jun 2021 12:00:50 +0200
Subject: [PATCH] Overwrite metadata from .cami

Fix #32, fix #31
---
 pyzebra/app/panel_hdf_viewer.py |  5 +----
 pyzebra/h5.py                   | 38 ++++++++++++++++++++++++++++-----
 2 files changed, 34 insertions(+), 9 deletions(-)

diff --git a/pyzebra/app/panel_hdf_viewer.py b/pyzebra/app/panel_hdf_viewer.py
index 735fb6a..95eca36 100644
--- a/pyzebra/app/panel_hdf_viewer.py
+++ b/pyzebra/app/panel_hdf_viewer.py
@@ -188,10 +188,7 @@ def create():
             # skip unnecessary update caused by selection drop
             return
 
-        det_data = pyzebra.read_detector_data(new[0])
-
-        if cami_meta and "crystal" in cami_meta:
-            det_data["ub"] = cami_meta["crystal"]["UB"]
+        det_data = pyzebra.read_detector_data(new[0], cami_meta)
 
         index_spinner.value = 0
         index_spinner.high = det_data["data"].shape[0] - 1
diff --git a/pyzebra/h5.py b/pyzebra/h5.py
index 8620df8..7c9998c 100644
--- a/pyzebra/h5.py
+++ b/pyzebra/h5.py
@@ -3,6 +3,7 @@ import numpy as np
 
 
 META_MATRIX = ("UB")
+META_CELL = ("cell")
 META_STR = ("name")
 
 def read_h5meta(filepath):
@@ -43,19 +44,21 @@ def parse_h5meta(file):
                     value = value.strip()
 
                     if variable in META_STR:
-                        content[section][variable] = value
+                        pass
+                    elif variable in META_CELL:
+                        value = np.array(value.split(",")[:6], dtype=np.float)
                     elif variable in META_MATRIX:
-                        ub_matrix = np.array(value.split(",")[:9], dtype=np.float).reshape(3, 3)
-                        content[section][variable] = ub_matrix
+                        value = np.array(value.split(",")[:9], dtype=np.float).reshape(3, 3)
                     else:  # default is a single float number
-                        content[section][variable] = float(value)
+                        value = float(value)
+                    content[section][variable] = value
             else:
                 content[section].append(line)
 
     return content
 
 
-def read_detector_data(filepath):
+def read_detector_data(filepath, cami_meta=None):
     """Read detector data and angles from an h5 file.
 
     Args:
@@ -78,6 +81,11 @@ def read_detector_data(filepath):
         else:
             det_data["zebra_mode"] = "nb"
 
+        # overwrite zebra_mode from cami
+        if cami_meta is not None:
+            if "zebra_mode" in cami_meta:
+                det_data["zebra_mode"] = cami_meta["zebra_mode"][0]
+
         # om, sometimes ph
         if det_data["zebra_mode"] == "nb":
             det_data["omega"] = h5f["/entry1/area_detector2/rotation_angle"][:]
@@ -91,6 +99,8 @@ def read_detector_data(filepath):
         det_data["chi"] = h5f["/entry1/sample/chi"][:]  # ch
         det_data["phi"] = h5f["/entry1/sample/phi"][:]  # ph
         det_data["ub"] = h5f["/entry1/sample/UB"][:].reshape(3, 3)
+        det_data["name"] = h5f["/entry1/sample/name"][0].decode()
+        det_data["cell"] = h5f["/entry1/sample/cell"][:]
 
         for var in ("omega", "gamma", "nu", "chi", "phi"):
             if abs(det_data[var][0] - det_data[var][-1]) > 0.1:
@@ -106,4 +116,22 @@ def read_detector_data(filepath):
         if "/entry1/sample/temperature" in h5f:
             det_data["temp"] = h5f["/entry1/sample/temperature"][:]
 
+        # overwrite metadata from .cami
+        if cami_meta is not None:
+            if "crystal" in cami_meta:
+                cami_meta_crystal = cami_meta["crystal"]
+                if "name" in cami_meta_crystal:
+                    det_data["name"] = cami_meta_crystal["name"]
+                if "UB" in cami_meta_crystal:
+                    det_data["ub"] = cami_meta_crystal["UB"]
+                if "cell" in cami_meta_crystal:
+                    det_data["cell"] = cami_meta_crystal["cell"]
+                if "lambda" in cami_meta_crystal:
+                    det_data["wave"] = cami_meta_crystal["lambda"]
+
+            if "detector parameters" in cami_meta:
+                cami_meta_detparam = cami_meta["detector parameters"]
+                if "dist1" in cami_meta_detparam:
+                    det_data["ddist"] = cami_meta_detparam["dist1"]
+
     return det_data