From c10efeb9ccf326f4c686e1d6d0b39d86aa6cbfb1 Mon Sep 17 00:00:00 2001
From: Ivan Usov <ivan.usov@psi.ch>
Date: Tue, 22 Jun 2021 11:23:38 +0200
Subject: [PATCH] Apply UB redefinition from .cami file

For #31
---
 pyzebra/app/panel_hdf_viewer.py | 12 ++++++++++--
 pyzebra/h5.py                   | 25 +++++++++++++++++++++++--
 2 files changed, 33 insertions(+), 4 deletions(-)

diff --git a/pyzebra/app/panel_hdf_viewer.py b/pyzebra/app/panel_hdf_viewer.py
index 2de7e62..d5ddc13 100644
--- a/pyzebra/app/panel_hdf_viewer.py
+++ b/pyzebra/app/panel_hdf_viewer.py
@@ -51,9 +51,11 @@ IMAGE_PLOT_H = int(IMAGE_H * 2) + 27
 
 def create():
     det_data = {}
+    cami_meta = {}
     roi_selection = {}
 
     def proposal_textinput_callback(_attr, _old, new):
+        nonlocal cami_meta
         proposal = new.strip()
         for zebra_proposals_path in pyzebra.ZEBRA_PROPOSALS_PATHS:
             proposal_path = os.path.join(zebra_proposals_path, proposal)
@@ -69,13 +71,16 @@ def create():
                 file_list.append((os.path.join(proposal_path, file), file))
         file_select.options = file_list
 
+        cami_meta = {}
+
     proposal_textinput = TextInput(title="Proposal number:", width=210)
     proposal_textinput.on_change("value", proposal_textinput_callback)
 
     def upload_button_callback(_attr, _old, new):
+        nonlocal cami_meta
         with io.StringIO(base64.b64decode(new).decode()) as file:
-            h5meta_list = pyzebra.parse_h5meta(file)
-            file_list = h5meta_list["filelist"]
+            cami_meta = pyzebra.parse_h5meta(file)
+            file_list = cami_meta["filelist"]
             file_select.options = [(entry, os.path.basename(entry)) for entry in file_list]
 
     upload_div = Div(text="or upload .cami file:", margin=(5, 5, 0, 5))
@@ -182,6 +187,9 @@ def create():
 
         det_data = pyzebra.read_detector_data(new[0])
 
+        if cami_meta and "crystal" in cami_meta:
+            det_data["ub"] = cami_meta["crystal"]["UB"]
+
         index_spinner.value = 0
         index_spinner.high = det_data["data"].shape[0] - 1
         index_slider.end = det_data["data"].shape[0] - 1
diff --git a/pyzebra/h5.py b/pyzebra/h5.py
index 23d2cff..8620df8 100644
--- a/pyzebra/h5.py
+++ b/pyzebra/h5.py
@@ -1,6 +1,10 @@
 import h5py
+import numpy as np
 
 
+META_MATRIX = ("UB")
+META_STR = ("name")
+
 def read_h5meta(filepath):
     """Open and parse content of a h5meta file.
 
@@ -23,13 +27,30 @@ def parse_h5meta(file):
         line = line.strip()
         if line.startswith("#begin "):
             section = line[len("#begin ") :]
-            content[section] = []
+            if section in ("detector parameters", "crystal"):
+                content[section] = {}
+            else:
+                content[section] = []
 
         elif line.startswith("#end"):
             section = None
 
         elif section:
-            content[section].append(line)
+            if section in ("detector parameters", "crystal"):
+                if "=" in line:
+                    variable, value = line.split("=", 1)
+                    variable = variable.strip()
+                    value = value.strip()
+
+                    if variable in META_STR:
+                        content[section][variable] = value
+                    elif variable in META_MATRIX:
+                        ub_matrix = np.array(value.split(",")[:9], dtype=np.float).reshape(3, 3)
+                        content[section][variable] = ub_matrix
+                    else:  # default is a single float number
+                        content[section][variable] = float(value)
+            else:
+                content[section].append(line)
 
     return content