Merged/developer

epoc-config.yaml

@@ -0,0 +1,42 @@
+# EPOC Redis Configuration
+
+# Experiment metadata
+affiliation: "YourInstitution"
+PI_name: "DefaultPI"
+project_id: "ProjectID"
+experiment_class: "External"
+measurement_tag: "sample1"
+
+# Data directories
+base_data_dir: "/data/jungfrau"
+XDS_template: "/path/to/XDS.INP"
+cal_dir: "/path/to/calibration"
+
+# Detector settings (e.g. of 1 Megapixel JUNGFRAU)
+nrows: 1064
+ncols: 1030
+threshold: 5
+
+# Viewer settings
+viewer_interval: 20.0
+viewer_cmin: 0.0
+viewer_cmax: 12000.0
+
+# Network endpoints
+jfjoch_host: "http://jungfrau-server:5232"      # Replace by the HTTP address of the Jungfraujoch web GUI
+receiver_endpoint: "tcp://jungfrau-server:5000" # look at the ZMQ stream endpoint in the Jungfraujoch Web GUI
+temserver: "temserver"                          # IP address of the TEM control machine (define in /etc/hosts)
+
+# Acquisition settings
+rotation_speed_idx: 0
+file_id: 0
+
+# Display overlays (optional)
+overlays:
+ - {'type': 'circle', 'xy': [526, 253], 'radius': 188, 'ec': 'r', 'fill': False, 'lw': 2}
+ - {'type': 'circle', 'xy': [526, 253], 'radius': 5, 'ec': 'g', 'fill': False, 'lw': 2}
+ - {'type': 'rectangle', 'xy': [574, 52], 'width': 60, 'height': 31, 'angle': 27.5, 'ec': 'y', 'fill': False}
+ - {'type': 'rectangle', 'xy': [0, 0], 'width': 1000, 'height': 1, 'angle': 19.8, 'ec': 'r', 'fill': False}
+
+# Used affiliations list
+usedAffiliations: ["YourInstitution", "External"]

init_redis.py

@@ -0,0 +1,11 @@
+from pathlib import Path
+from epoc import ConfigurationClient, auth_token, redis_host
+
+# Connect to Redis
+cfg = ConfigurationClient(redis_host(), token=auth_token())
+
+# Load configuration from YAML (flush_db=True clears any existing data)
+cfg.from_yaml(Path('epoc-config.yaml'), flush_db=True)
+
+print("Redis database initialized successfully!")
+print(cfg)

jungfrau_gui/globals.py

@@ -1,7 +1,6 @@
 import ctypes
 import numpy as np
 import multiprocessing as mp
-from epoc import ConfigurationClient, auth_token, redis_host
 import subprocess
 
 def get_git_info():
@@ -49,46 +48,113 @@ def get_git_info():
         # Git not installed or command failed
         return defaults
 
-cfg = ConfigurationClient(redis_host(), token=auth_token())
+# ----------------------------
+# Runtime-configurable globals
+# ----------------------------
 stream = "tcp://localhost:4545"
 tem_mode = True
-# jfj = False
+tem_host = "localhost"
+tem_port = 3535
 
-tem_host = cfg.temserver
 dev = False
-#Configuration
-nrow = cfg.nrows 
-ncol = cfg.ncols
+
+nrow = 0
+ncol = 0
 
 dtype = np.float32
 cdtype = ctypes.c_float
 
-# fitterWorkerReady = mp.Value(ctypes.c_bool)
-# fitterWorkerReady.value = False
-
 accframes = 0
-acc_image = np.zeros((nrow,ncol), dtype = dtype)
+acc_image = np.zeros((0, 0), dtype=dtype)  # allocated properly in init()
 
 exit_flag = mp.Value(ctypes.c_bool)
 exit_flag.value = False
 
-#Data type to write to file
+# Data type to write to file
 file_dt = np.int32
 
-#Data type to receive from the stream
+# Data type to receive from the stream
 stream_dt = np.float32
 
 # Flags for non-updated magnification values in MAG and DIFF modes
-mag_value_img = [1, 'X', 'X1']
-mag_value_diff = [1, 'mm', '1cm']
+mag_value_img = [1, "X", "X1"]
+mag_value_diff = [1, "mm", "1cm"]
 
-tag, branch, commit  = get_git_info()
+# Version info (safe at import; no Redis!)
+tag, branch, commit = get_git_info()
 
 # constants, presets
-UM_TO_NM = 1e3
-MM_TO_UM = 1e3
-KV_TO_V = 1e3 
+UM_TO_NM = MM_TO_UM = MS_TO_US = S_TO_MS = KV_TO_V = 1e3 
 PIXEL = 0.075 # mm
 
+# TEM control variables
 default_HT = 200000.00 # V
+# Backlash correction (KT)
 backlash = [100, 80, 0, 0]
+# overshoot/preload used for two-step jog moves
+preload  = [2000, 2000, 0, 1]  # X,Y,Z in nm (2 µm), TX in deg (1°)
+
+min_mag_for_mag = 1500 # border between LowMag/Mag
+
+## safety not to hit hardware-limit
+click_on_move_thresholds = {'dxy_min': 0.3, 'dxy_max': 100, 
+                            'dz_min_mag': 1, 'dz_max_mag': 10,
+                            'dz_min_lmag': 3, 'absz_min': -70, 'absz_max': 20}
+
+## stage shift larger than these values will be hold in history
+stage_relaxation_thresholds = [30, 30, 30, 0.2, 100] # nm, nm, nm, deg., deg. 
+
+## software limit for GATAN holder. Smaller value (~65) may be necessary for complete safety (e.g. remote-operation).
+max_stage_tilt = 72
+default_roation_end = 60
+
+## variabls for autofocusing
+IL1_0 = 21780 # 21819 
+ILS_0 = [32920, 32776] # [32820, 32976]
+WAIT_TIME_S = 0.25 # TODO: optimize value
+
+
+# Frame control variables
+default_polling_frequency = 1000
+min_polling_frequency = 100 # safety not to inquire TEM-values too frequently
+max_polling_frequency = 10000
+
+default_frame_summed = 100
+default_image_time_us = 500
+min_frame_summed = 10 # safety not to save unexpectedly large datasets
+max_frame_summed = 1000
+detector_freq = 2000
+max_duration = 3600 # sec
+
+
+# Communication variables
+dataserver_host = "noether"
+dataserver_port = 3463
+
+max_retries_tagging = 3
+inquiry_delay = 0.1 # sec
+
+
+def init(*, stream_, dtype_, cdtype_, tem_mode_, tem_host_, dev_, nrow_, ncol_):
+    """
+    Initialize globals that previously depended on Redis at import-time.
+
+    Call this exactly once in launch_gui.py *before* importing modules that use globals.
+    """
+    global stream, dtype, cdtype, tem_mode, tem_host, dev, nrow, ncol, acc_image
+
+    stream = stream_
+    dtype = np.dtype(dtype_)
+    cdtype = cdtype_
+
+    tem_mode = bool(tem_mode_)
+    tem_host = str(tem_host_)
+    dev = bool(dev_)
+
+    nrow = int(nrow_)
+    ncol = int(ncol_)
+
+    if nrow <= 0 or ncol <= 0:
+        raise ValueError(f"Invalid detector geometry: nrow={nrow}, ncol={ncol}")
+
+    acc_image = np.zeros((nrow, ncol), dtype=dtype)