diff --git a/csaxs_bec/bec_ipython_client/plugins/LamNI/LamNI.png b/csaxs_bec/bec_ipython_client/plugins/LamNI/LamNI.png
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index 0000000..e8aaba2
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diff --git a/csaxs_bec/bec_ipython_client/plugins/LamNI/LamNI_logo.png b/csaxs_bec/bec_ipython_client/plugins/LamNI/LamNI_logo.png
deleted file mode 100644
index 965195c..0000000
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diff --git a/csaxs_bec/bec_ipython_client/plugins/flomni/flOMNI.png b/csaxs_bec/bec_ipython_client/plugins/flomni/flOMNI.png
new file mode 100644
index 0000000..b6972b0
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diff --git a/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py b/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py
index f36a346..f2da35d 100644
--- a/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py
+++ b/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py
@@ -969,8 +969,6 @@ class FlomniSampleTransferMixin:
class FlomniAlignmentMixin:
import csaxs_bec
- import os
- from pathlib import Path
# Ensure this is a Path object, not a string
csaxs_bec_basepath = Path(csaxs_bec.__file__)
@@ -1211,6 +1209,76 @@ class FlomniAlignmentMixin:
return additional_correction_shift
+class _ProgressProxy:
+ """Dict-like proxy that persists the flOMNI progress dict as a BEC global variable.
+
+ Every read (`proxy["key"]`) fetches the current dict from the global var store,
+ and every write (`proxy["key"] = val`) fetches, updates, and saves it back.
+ This makes the progress state visible to all BEC client sessions via
+ ``client.get_global_var("tomo_progress")``.
+ """
+
+ _GLOBAL_VAR_KEY = "tomo_progress"
+ _DEFAULTS: dict = {
+ "subtomo": 0,
+ "subtomo_projection": 0,
+ "subtomo_total_projections": 1,
+ "projection": 0,
+ "total_projections": 1,
+ "angle": 0,
+ "tomo_type": 0,
+ "tomo_start_time": None,
+ "estimated_remaining_time": None,
+ "heartbeat": None,
+ }
+
+ def __init__(self, client):
+ self._client = client
+
+ # ------------------------------------------------------------------
+ # Internal helpers
+ # ------------------------------------------------------------------
+ def _load(self) -> dict:
+ val = self._client.get_global_var(self._GLOBAL_VAR_KEY)
+ if val is None:
+ return dict(self._DEFAULTS)
+ return val
+
+ def _save(self, data: dict) -> None:
+ self._client.set_global_var(self._GLOBAL_VAR_KEY, data)
+
+ # ------------------------------------------------------------------
+ # Dict-like interface
+ # ------------------------------------------------------------------
+ def __getitem__(self, key):
+ return self._load()[key]
+
+ def __setitem__(self, key, value) -> None:
+ data = self._load()
+ data[key] = value
+ self._save(data)
+
+ def __repr__(self) -> str:
+ return f"{self.__class__.__name__}({self._load()!r})"
+
+ def get(self, key, default=None):
+ return self._load().get(key, default)
+
+ def update(self, *args, **kwargs) -> None:
+ """Update multiple fields in a single round-trip."""
+ data = self._load()
+ data.update(*args, **kwargs)
+ self._save(data)
+
+ def reset(self) -> None:
+ """Reset all progress fields to their default values."""
+ self._save(dict(self._DEFAULTS))
+
+ def as_dict(self) -> dict:
+ """Return a plain copy of the current progress state."""
+ return self._load()
+
+
class Flomni(
FlomniInitStagesMixin,
FlomniSampleTransferMixin,
@@ -1233,14 +1301,8 @@ class Flomni(
self.corr_angle_y = []
self.corr_pos_y_2 = []
self.corr_angle_y_2 = []
- self.progress = {}
- self.progress["subtomo"] = 0
- self.progress["subtomo_projection"] = 0
- self.progress["subtomo_total_projections"] = 1
- self.progress["projection"] = 0
- self.progress["total_projections"] = 1
- self.progress["angle"] = 0
- self.progress["tomo_type"] = 0
+ self._progress_proxy = _ProgressProxy(self.client)
+ self._progress_proxy.reset()
self.OMNYTools = OMNYTools(self.client)
self.reconstructor = PtychoReconstructor(self.ptycho_reconstruct_foldername)
self.tomo_id_manager = TomoIDManager()
@@ -1296,6 +1358,42 @@ class Flomni(
self.special_angles = []
self.special_angle_repeats = 1
+ @property
+ def progress(self) -> _ProgressProxy:
+ """Proxy dict backed by the BEC global variable ``tomo_progress``.
+
+ Readable from any BEC client session via::
+
+ client.get_global_var("tomo_progress")
+
+ Individual fields can be read and written just like a regular dict::
+
+ flomni.progress["projection"] # read
+ flomni.progress["projection"] = 42 # write (persists immediately)
+
+ To update multiple fields atomically use :py:meth:`_ProgressProxy.update`::
+
+ flomni.progress.update(projection=42, angle=90.0)
+
+ To reset all fields to their defaults::
+
+ flomni.progress.reset()
+ """
+ return self._progress_proxy
+
+ @progress.setter
+ def progress(self, val: dict) -> None:
+ """Replace the entire progress dict.
+
+ Accepts a plain :class:`dict` and persists it to the global var store.
+ Example::
+
+ flomni.progress = {"projection": 0, "total_projections": 100, ...}
+ """
+ if not isinstance(val, dict):
+ raise TypeError(f"progress must be a dict, got {type(val).__name__!r}")
+ self._progress_proxy._save(val)
+
@property
def tomo_shellstep(self):
val = self.client.get_global_var("tomo_shellstep")
@@ -1482,21 +1580,11 @@ class Flomni(
def sample_name(self):
return self.sample_get_name(0)
- def write_to_scilog(self, content, tags: list = None):
- try:
- if tags is not None:
- tags.append("BEC")
- else:
- tags = ["BEC"]
- msg = bec.logbook.LogbookMessage()
- msg.add_text(content).add_tag(tags)
- self.client.logbook.send_logbook_message(msg)
- except Exception:
- logger.warning("Failed to write to scilog.")
-
def tomo_alignment_scan(self):
"""
Performs a tomogram alignment scan.
+ Collects all scan numbers acquired during the alignment, prints them at the end,
+ and creates a BEC scilog text entry summarising the alignment scan numbers.
"""
if self.get_alignment_offset(0) == (0, 0, 0):
print("It appears that the xrayeye alignemtn was not performend or loaded. Aborting.")
@@ -1506,11 +1594,9 @@ class Flomni(
self.feye_out()
tags = ["BEC_alignment_tomo", self.sample_name]
- self.write_to_scilog(
- f"Starting alignment scan. First scan number: {bec.queue.next_scan_number}.", tags
- )
start_angle = 0
+ alignment_scan_numbers = []
angle_end = start_angle + 180
for angle in np.linspace(start_angle, angle_end, num=int(180 / 45) + 1, endpoint=True):
@@ -1522,7 +1608,6 @@ class Flomni(
try:
start_scan_number = bec.queue.next_scan_number
self.tomo_scan_projection(angle)
- self.tomo_reconstruct()
error_caught = False
except AlarmBase as exc:
if exc.alarm_type == "TimeoutError":
@@ -1536,24 +1621,27 @@ class Flomni(
end_scan_number = bec.queue.next_scan_number
for scan_nr in range(start_scan_number, end_scan_number):
- self._write_tomo_scan_number(scan_nr, angle, 0)
+ #self._write_tomo_scan_number(scan_nr, angle, 0)
+ alignment_scan_numbers.append(scan_nr)
umv(dev.fsamroy, 0)
self.OMNYTools.printgreenbold(
"\n\nAlignment scan finished. Please run SPEC_ptycho_align and load the new fit by flomni.read_alignment_offset() ."
)
- def _write_subtomo_to_scilog(self, subtomo_number):
- dev = builtins.__dict__.get("dev")
- bec = builtins.__dict__.get("bec")
- if self.tomo_id > 0:
- tags = ["BEC_subtomo", self.sample_name, f"tomo_id_{self.tomo_id}"]
- else:
- tags = ["BEC_subtomo", self.sample_name]
- self.write_to_scilog(
- f"Starting subtomo: {subtomo_number}. First scan number: {bec.queue.next_scan_number}.",
- tags,
+ # summary of alignment scan numbers
+ scan_list_str = ", ".join(str(s) for s in alignment_scan_numbers)
+ #print(f"\nAlignment scan numbers ({len(alignment_scan_numbers)} total): {scan_list_str}")
+
+ # BEC scilog entry (no logo)
+ scilog_content = (
+ f"Alignment scan finished.\n"
+ f"Sample: {self.sample_name}\n"
+ f"Number of alignment scans: {len(alignment_scan_numbers)}\n"
+ f"Alignment scan numbers: {scan_list_str}\n"
)
+ print(scliog_content)
+ bec.messaging.scilog.new().add_text(scilog_content.replace("\n", "
")).add_tags("alignmentscan").send()
def sub_tomo_scan(self, subtomo_number, start_angle=None):
"""
@@ -1562,18 +1650,6 @@ class Flomni(
subtomo_number (int): The sub tomogram number.
start_angle (float, optional): The start angle of the scan. Defaults to None.
"""
- # dev = builtins.__dict__.get("dev")
- # bec = builtins.__dict__.get("bec")
- # if self.tomo_id > 0:
- # tags = ["BEC_subtomo", self.sample_name, f"tomo_id_{self.tomo_id}"]
- # else:
- # tags = ["BEC_subtomo", self.sample_name]
- # self.write_to_scilog(
- # f"Starting subtomo: {subtomo_number}. First scan number: {bec.queue.next_scan_number}.",
- # tags,
- # )
-
- self._write_subtomo_to_scilog(subtomo_number)
if start_angle is not None:
print(f"Sub tomo scan with start angle {start_angle} requested.")
@@ -1673,6 +1749,7 @@ class Flomni(
successful = False
error_caught = False
if 0 <= angle < 180.05:
+ self.progress["heartbeat"] = datetime.datetime.now().isoformat()
print(f"Starting flOMNI scan for angle {angle} in subtomo {subtomo_number}")
self._print_progress()
while not successful:
@@ -1746,6 +1823,8 @@ class Flomni(
# self.write_pdf_report()
# else:
self.tomo_id = 0
+ self.write_pdf_report()
+ self.progress["tomo_start_time"] = datetime.datetime.now().isoformat()
with scans.dataset_id_on_hold:
if self.tomo_type == 1:
@@ -1765,7 +1844,6 @@ class Flomni(
while True:
angle, subtomo_number = self._golden(ii, self.golden_ratio_bunch_size, 180, 1)
if previous_subtomo_number != subtomo_number:
- self._write_subtomo_to_scilog(subtomo_number)
if (
subtomo_number % 2 == 1
and ii > 10
@@ -1813,7 +1891,6 @@ class Flomni(
ii, int(180 / self.tomo_angle_stepsize), 180, 1, 0
)
if previous_subtomo_number != subtomo_number:
- self._write_subtomo_to_scilog(subtomo_number)
if (
subtomo_number % 2 == 1
and ii > 10
@@ -1855,14 +1932,42 @@ class Flomni(
self._print_progress()
self.OMNYTools.printgreenbold("Tomoscan finished")
+ @staticmethod
+ def _format_duration(seconds: float) -> str:
+ """Format a duration in seconds as a human-readable string, e.g. '2h 03m 15s'."""
+ seconds = int(seconds)
+ h, remainder = divmod(seconds, 3600)
+ m, s = divmod(remainder, 60)
+ if h > 0:
+ return f"{h}h {m:02d}m {s:02d}s"
+ if m > 0:
+ return f"{m}m {s:02d}s"
+ return f"{s}s"
+
def _print_progress(self):
+ # --- compute and store estimated remaining time -----------------------
+ start_str = self.progress.get("tomo_start_time")
+ projection = self.progress["projection"]
+ total = self.progress["total_projections"]
+ if start_str is not None and total > 0 and projection > 9:
+ elapsed = (
+ datetime.datetime.now() - datetime.datetime.fromisoformat(start_str)
+ ).total_seconds()
+ rate = projection / elapsed # projections per second
+ remaining_s = (total - projection) / rate
+ self.progress["estimated_remaining_time"] = remaining_s
+ eta_str = self._format_duration(remaining_s)
+ else:
+ eta_str = "N/A"
+ # ----------------------------------------------------------------------
print("\x1b[95mProgress report:")
print(f"Tomo type: ....................... {self.progress['tomo_type']}")
print(f"Projection: ...................... {self.progress['projection']:.0f}")
print(f"Total projections expected ....... {self.progress['total_projections']}")
print(f"Angle: ........................... {self.progress['angle']}")
print(f"Current subtomo: ................. {self.progress['subtomo']}")
- print(f"Current projection within subtomo: {self.progress['subtomo_projection']}\x1b[0m")
+ print(f"Current projection within subtomo: {self.progress['subtomo_projection']}")
+ print(f"Estimated remaining time: ........ {eta_str}\x1b[0m")
self._flomnigui_update_progress()
def add_sample_database(
@@ -1886,7 +1991,6 @@ class Flomni(
return
self.tomo_scan_projection(angle)
- self.tomo_reconstruct()
def _golden(self, ii, howmany_sorted, maxangle, reverse=False):
"""returns the iis golden ratio angle of sorted bunches of howmany_sorted and its subtomo number"""
@@ -1991,7 +2095,7 @@ class Flomni(
f"{str(datetime.datetime.now())}: flomni scan projection at angle {angle}, scan"
f" number {bec.queue.next_scan_number}.\n"
)
- # self.write_to_scilog(log_message, ["BEC_scans", self.sample_name])
+
scans.flomni_fermat_scan(
fovx=self.fovx,
fovy=self.fovy,
@@ -2004,6 +2108,9 @@ class Flomni(
corridor_size=corridor_size,
)
+ self.tomo_reconstruct()
+
+
def tomo_parameters(self):
"""print and update the tomo parameters"""
print("Current settings:")
@@ -2145,38 +2252,58 @@ class Flomni(
fovxy = f"{self.fovx:.2f}/{self.fovy:.2f}"
stitching = f"{self.stitch_x:.2f}/{self.stitch_y:.2f}"
dataset_id = str(self.client.queue.next_dataset_number)
+ account = bec.active_account
content = [
f"{'Sample Name:':<{padding}}{self.sample_name:>{padding}}\n",
f"{'Measurement ID:':<{padding}}{str(self.tomo_id):>{padding}}\n",
f"{'Dataset ID:':<{padding}}{dataset_id:>{padding}}\n",
f"{'Sample Info:':<{padding}}{'Sample Info':>{padding}}\n",
- f"{'e-account:':<{padding}}{str(self.client.username):>{padding}}\n",
+ f"{'e-account:':<{padding}}{str(account):>{padding}}\n",
f"{'Number of projections:':<{padding}}{int(180 / self.tomo_angle_stepsize * 8):>{padding}}\n",
f"{'First scan number:':<{padding}}{self.client.queue.next_scan_number:>{padding}}\n",
f"{'Last scan number approx.:':<{padding}}{self.client.queue.next_scan_number + int(180 / self.tomo_angle_stepsize * 8) + 10:>{padding}}\n",
- f"{'Current photon energy:':<{padding}}{dev.mokev.read()['mokev']['value']:>{padding}.4f}\n",
+ f"{'Current photon energy:':<{padding}}To be implemented\n",
+ #f"{'Current photon energy:':<{padding}}{dev.mokev.read()['mokev']['value']:>{padding}.4f}\n",
f"{'Exposure time:':<{padding}}{self.tomo_countingtime:>{padding}.2f}\n",
f"{'Fermat spiral step size:':<{padding}}{self.tomo_shellstep:>{padding}.2f}\n",
f"{'FOV:':<{padding}}{fovxy:>{padding}}\n",
- f"{'Stitching:':<{padding}}{stitching:>{padding}}\n",
+ f"{'Stitching:':<{padding}}{stitching:>{padding}.0f}\n",
f"{'Number of individual sub-tomograms:':<{padding}}{8:>{padding}}\n",
f"{'Angular step within sub-tomogram:':<{padding}}{self.tomo_angle_stepsize:>{padding}.2f}\n",
]
content = "".join(content)
- user_target = os.path.expanduser(f"~/Data10/documentation/tomo_scan_ID_{self.tomo_id}.pdf")
+ user_target = os.path.expanduser(f"~/data/raw/documentation/tomo_scan_ID_{self.tomo_id}.pdf")
with PDFWriter(user_target) as file:
file.write(header)
file.write(content)
- subprocess.run(
- "xterm /work/sls/spec/local/XOMNY/bin/upload/upload_last_pon.sh &", shell=True
- )
+ # subprocess.run(
+ # "xterm /work/sls/spec/local/XOMNY/bin/upload/upload_last_pon.sh &", shell=True
+ # )
# status = subprocess.run(f"cp /tmp/spec-e20131-specES1.pdf {user_target}", shell=True)
- msg = bec.logbook.LogbookMessage()
- logo_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "LamNI_logo.png")
- msg.add_file(logo_path).add_text("".join(content).replace("\n", "")).add_tag(
- ["BEC", "tomo_parameters", f"dataset_id_{dataset_id}", "LamNI", self.sample_name]
- )
- self.client.logbook.send_logbook_message(msg)
+ # msg = bec.tomo_progress.tomo_progressMessage()
+ # logo_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "LamNI_logo.png")
+ # msg.add_file(logo_path).add_text("".join(content).replace("\n", "
")).add_tag(
+ # ["BEC", "tomo_parameters", f"dataset_id_{dataset_id}", "flOMNI", self.sample_name]
+ # )
+ # self.client.tomo_progress.send_tomo_progress_message("~/data/raw/documentation/tomo_scan_ID_{self.tomo_id}.pdf").send()
+ import csaxs_bec
+
+
+ # Ensure this is a Path object, not a string
+ csaxs_bec_basepath = Path(csaxs_bec.__file__)
+
+ logo_file_rel = "flOMNI.png"
+
+ # Build the absolute path correctly
+ logo_file = (
+ csaxs_bec_basepath.parent
+ / "bec_ipython_client"
+ / "plugins"
+ / "flomni"
+ / logo_file_rel
+ ).resolve()
+ print(logo_file)
+ bec.messaging.scilog.new().add_attachment(logo_file, width=200).add_text(content.replace("\n", "
")).add_tags("tomoscan").send()
if __name__ == "__main__":
diff --git a/csaxs_bec/bec_ipython_client/plugins/flomni/gui_tools.py b/csaxs_bec/bec_ipython_client/plugins/flomni/gui_tools.py
index 653883f..5d03537 100644
--- a/csaxs_bec/bec_ipython_client/plugins/flomni/gui_tools.py
+++ b/csaxs_bec/bec_ipython_client/plugins/flomni/gui_tools.py
@@ -223,6 +223,14 @@ class flomniGuiTools:
self._flomnigui_update_progress()
def _flomnigui_update_progress(self):
+ """Update the progress ring bar and center label from the current progress state.
+
+ ``self.progress`` is backed by the BEC global variable ``tomo_progress``
+ (see :class:`_ProgressProxy` in ``flomni.py``), so this method reflects
+ the live state that is also accessible from other BEC client sessions via::
+
+ client.get_global_var("tomo_progress")
+ """
main_progress_ring = self.progressbar.rings[0]
subtomo_progress_ring = self.progressbar.rings[1]
if self.progressbar is not None:
@@ -235,6 +243,31 @@ class flomniGuiTools:
main_progress_ring.set_value(progress)
subtomo_progress_ring.set_value(subtomo_progress)
+ # --- format start time for display --------------------------------
+ start_str = self.progress.get("tomo_start_time")
+ if start_str is not None:
+ import datetime as _dt
+ start_display = _dt.datetime.fromisoformat(start_str).strftime("%Y-%m-%d %H:%M:%S")
+ else:
+ start_display = "N/A"
+
+ # --- format estimated remaining time ------------------------------
+ remaining_s = self.progress.get("estimated_remaining_time")
+ if remaining_s is not None and remaining_s >= 0:
+ import datetime as _dt
+ remaining_s = int(remaining_s)
+ h, rem = divmod(remaining_s, 3600)
+ m, s = divmod(rem, 60)
+ if h > 0:
+ eta_display = f"{h}h {m:02d}m {s:02d}s"
+ elif m > 0:
+ eta_display = f"{m}m {s:02d}s"
+ else:
+ eta_display = f"{s}s"
+ else:
+ eta_display = "N/A"
+ # ------------------------------------------------------------------
+
text = (
f"Progress report:\n"
f" Tomo type: {self.progress['tomo_type']}\n"
@@ -243,7 +276,9 @@ class flomniGuiTools:
f" Angle: {self.progress['angle']:.1f}\n"
f" Current subtomo: {self.progress['subtomo']}\n"
f" Current projection within subtomo: {self.progress['subtomo_projection']}\n"
- f" Total projections per subtomo: {int(self.progress['subtomo_total_projections'])}"
+ f" Total projections per subtomo: {int(self.progress['subtomo_total_projections'])}\n"
+ f" Scan started: {start_display}\n"
+ f" Est. remaining: {eta_display}"
)
self.progressbar.set_center_label(text)
diff --git a/csaxs_bec/bec_ipython_client/plugins/omny/OMNY.png b/csaxs_bec/bec_ipython_client/plugins/omny/OMNY.png
new file mode 100644
index 0000000..bf00a11
Binary files /dev/null and b/csaxs_bec/bec_ipython_client/plugins/omny/OMNY.png differ