From c0831210c801c7238d5417ecdaa3e2da35523a73 Mon Sep 17 00:00:00 2001
From: gac-x02da <gac-x02da@x02da-bec-001.psi.ch>
Date: Mon, 16 Jun 2025 21:21:40 +0200
Subject: [PATCH 01/10] wip

---
 .../devices/std_daq/std_daq_live_processing.py       |  3 ++-
 tomcat_bec/scans/simple_scans.py                     | 12 ++++--------
 2 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/tomcat_bec/devices/std_daq/std_daq_live_processing.py b/tomcat_bec/devices/std_daq/std_daq_live_processing.py
index 9f3f491..714c5ea 100644
--- a/tomcat_bec/devices/std_daq/std_daq_live_processing.py
+++ b/tomcat_bec/devices/std_daq/std_daq_live_processing.py
@@ -122,8 +122,9 @@ class StdDaqLiveProcessing:
             return corrected_data
 
         # Ensure that the division does not lead to division by zero
+        flat_corr = np.abs(flat-dark)
         corrected_data = np.divide(
-            data - dark, flat - dark, out=np.zeros_like(data), where=(flat - dark) != 0
+            data - dark, flat_corr, out=np.zeros_like(data, dtype=np.float32), where=flat_corr != 0
         )
         return corrected_data
 
diff --git a/tomcat_bec/scans/simple_scans.py b/tomcat_bec/scans/simple_scans.py
index 243aa05..06a9358 100644
--- a/tomcat_bec/scans/simple_scans.py
+++ b/tomcat_bec/scans/simple_scans.py
@@ -102,12 +102,10 @@ class TomoComponents:
         self.connector.send_client_info(f"Acquiring {num_images} dark images.")
 
         yield from self.restart_cameras(
-            name=name, prefix=name, num_images=num_images, frames_per_trigger=1
+            name=name, prefix=name, num_images=num_images, frames_per_trigger=num_images
         )
         # yield from self.close_shutter()
-        for i in range(num_images):
-            logger.debug(f"Acquiring dark image {i+1}/{num_images}.")
-            yield from self.stubs.trigger(min_wait=exposure_time)
+        yield from self.stubs.trigger(min_wait=exposure_time)
         yield from self.complete()
         yield from self.update_live_processing_references(ref_type="dark")
         yield from self.restore_configs(name=name)
@@ -130,12 +128,10 @@ class TomoComponents:
         self.connector.send_client_info(f"Acquiring {num_images} flat images.")
 
         yield from self.restart_cameras(
-            name=name, prefix=name, num_images=num_images, frames_per_trigger=1
+            name=name, prefix=name, num_images=num_images, frames_per_trigger=num_images
         )
         # yield from self.open_shutter()
-        for i in range(num_images):
-            logger.debug(f"Acquiring flat image {i+1}/{num_images}.")
-            yield from self.stubs.trigger(min_wait=exposure_time)
+        yield from self.stubs.trigger(min_wait=exposure_time)
         yield from self.complete()
         yield from self.update_live_processing_references(ref_type="flat")
         yield from self.restore_configs(name=name)
-- 
2.49.1


From f49018754e302cb3e39361cffd10144419a88b4f Mon Sep 17 00:00:00 2001
From: wakonig_k <klaus.wakonig@psi.ch>
Date: Mon, 16 Jun 2025 21:26:58 +0200
Subject: [PATCH 02/10] wip

---
 tomcat_bec/scans/simple_scans.py | 39 +++++++++++++++++++++++++++++++-
 1 file changed, 38 insertions(+), 1 deletion(-)

diff --git a/tomcat_bec/scans/simple_scans.py b/tomcat_bec/scans/simple_scans.py
index 06a9358..ad22654 100644
--- a/tomcat_bec/scans/simple_scans.py
+++ b/tomcat_bec/scans/simple_scans.py
@@ -70,7 +70,7 @@ class TomoComponents:
         for cam in self.cameras:
             yield from self.stubs.send_rpc_and_wait(
                 device=cam, func_name="restore_config", name=name
-            )            
+            )
 
     def update_live_processing_references(self, ref_type: Literal["dark", "flat"]):
         """
@@ -143,6 +143,43 @@ class TomoComponents:
         yield from self.acquire_flat(num_flats, exposure_time=exp_time, name=name)
 
 
+class AcquireDark(ScanBase):
+    scan_name = "acquire_dark"
+
+    def __init__(self, exp_time: float, frames_per_trigger: int = 1, **kwargs):
+        """
+        Acquire dark images.
+
+        Args:
+            num_images (int): Number of dark images to acquire.
+            exposure_time (float): Exposure time for each dark image in seconds.
+            name (str): Name for the dark image acquisition. Default: "dark"
+
+        Returns:
+            ScanReport
+        """
+        super().__init__(frames_per_trigger=frames_per_trigger, exp_time=exp_time, **kwargs)
+        self.components = TomoComponents(self)
+
+    def scan_report_instructions(self):
+        """
+        Generate scan report instructions for the dark image acquisition.
+        This method provides the necessary instructions to listen to the camera progress during the scan.
+        """
+        if not self.components.cameras:
+            yield from super().scan_report_instructions()
+            return
+
+        # Use the first camera or "gfcam" if available for reporting
+        report_camera = (
+            "gfcam" if "gfcam" in self.components.cameras else self.components.cameras[0]
+        )
+        yield from self.stubs.scan_report_instruction({"device_progress": [report_camera]})
+
+    def scan_core(self):
+        yield from self.components.acquire_dark(self.frames_per_trigger, self.exp_time, name="dark")
+
+
 class TomoScan(LineScan):
     scan_name = "tomo_line_scan"
 
-- 
2.49.1


From a9b275c0b9628b9ee40666291451c06a0f5bf938 Mon Sep 17 00:00:00 2001
From: gac-x02da <gac-x02da@x02da-bec-001.psi.ch>
Date: Mon, 16 Jun 2025 22:20:42 +0200
Subject: [PATCH 03/10] wip

---
 tomcat_bec/devices/pco_edge/pcoedgecamera.py |   9 +-
 tomcat_bec/scans/__init__.py                 |  16 +--
 tomcat_bec/scans/simple_scans.py             | 113 ++++++++++++++-----
 3 files changed, 99 insertions(+), 39 deletions(-)

diff --git a/tomcat_bec/devices/pco_edge/pcoedgecamera.py b/tomcat_bec/devices/pco_edge/pcoedgecamera.py
index 75ea0cb..2bc810e 100644
--- a/tomcat_bec/devices/pco_edge/pcoedgecamera.py
+++ b/tomcat_bec/devices/pco_edge/pcoedgecamera.py
@@ -434,11 +434,16 @@ class PcoEdge5M(PSIDeviceBase, PcoEdgeBase):
                 "/gpfs/test/test-beamline"  # FIXME: This should be from the scan message
             )
         if "file_prefix" not in scan_args:
-            scan_args["file_prefix"] = scan_msg.info["file_components"][0].split("/")[-1] + "_"
+            file_base = scan_msg.info["file_components"][0].split("/")[-1]
+            file_suffix = scan_msg.info.get("file_suffix") or ""
+            comps = [file_base, self.name]
+            if file_suffix:
+                comps.append(file_suffix)
+            scan_args["file_prefix"] = "_".join(comps)
         self.configure(scan_args)
 
         if scan_msg.scan_type == "step":
-            num_points = self.frames_per_trigger.get() * scan_msg.num_points  # type: ignore
+            num_points = self.frames_per_trigger.get() * max(scan_msg.num_points, 1)  # type: ignore
         else:
             num_points = self.frames_per_trigger.get()
 
diff --git a/tomcat_bec/scans/__init__.py b/tomcat_bec/scans/__init__.py
index ad3c815..fdb7f1f 100644
--- a/tomcat_bec/scans/__init__.py
+++ b/tomcat_bec/scans/__init__.py
@@ -1,9 +1,9 @@
-from .simple_scans import TomoFlyScan, TomoScan
+from .simple_scans import TomoFlyScan, TomoScan, AcquireDark
 from .tomcat_scans import TomcatSimpleSequence, TomcatSnapNStep
-from .tutorial_fly_scan import (
-    AcquireDark,
-    AcquireProjections,
-    AcquireRefs,
-    AcquireWhite,
-    TutorialFlyScanContLine,
-)
+# from .tutorial_fly_scan import (
+#     # AcquireDark,
+#     AcquireProjections,
+#     AcquireRefs,
+#     AcquireWhite,
+#     TutorialFlyScanContLine,
+# )
diff --git a/tomcat_bec/scans/simple_scans.py b/tomcat_bec/scans/simple_scans.py
index ad22654..96a758a 100644
--- a/tomcat_bec/scans/simple_scans.py
+++ b/tomcat_bec/scans/simple_scans.py
@@ -62,6 +62,21 @@ class TomoComponents:
                 frames_per_trigger=frames_per_trigger,
             )
 
+    def scan_report_instructions(self):
+        """
+        Generate scan report instructions for the dark image acquisition.
+        This method provides the necessary instructions to listen to the camera progress during the scan.
+        """
+        if not self.components.cameras:
+            yield from super().scan_report_instructions()
+            return
+
+        # Use the first camera or "gfcam" if available for reporting
+        report_camera = (
+            "gfcam" if "gfcam" in self.components.cameras else self.components.cameras[0]
+        )
+        yield from self.stubs.scan_report_instruction({"device_progress": [report_camera]})
+
     def complete(self):
         for cam in self.cameras:
             yield from self.stubs.send_rpc_and_wait(device=cam, func_name="on_complete")
@@ -88,7 +103,7 @@ class TomoComponents:
                 device=cam, func_name="update_live_processing_reference", reference_type=ref_type
             )
 
-    def acquire_dark(self, num_images: int, exposure_time: float, name="dark"):
+    def acquire_dark(self, num_images: int, exposure_time: float, name="dark", restart=True):
         """
         Acquire dark images.
 
@@ -101,20 +116,22 @@ class TomoComponents:
         logger.info(f"Acquiring {num_images} dark images with exposure time {exposure_time}s.")
         self.connector.send_client_info(f"Acquiring {num_images} dark images.")
 
-        yield from self.restart_cameras(
-            name=name, prefix=name, num_images=num_images, frames_per_trigger=num_images
-        )
+        if restart:
+            yield from self.restart_cameras(
+                name=name, prefix=name, num_images=num_images, frames_per_trigger=num_images
+            )
         # yield from self.close_shutter()
         yield from self.stubs.trigger(min_wait=exposure_time)
         yield from self.complete()
         yield from self.update_live_processing_references(ref_type="dark")
-        yield from self.restore_configs(name=name)
+        if restart:
+            yield from self.restore_configs(name=name)
 
         # yield from self.open_shutter()
         self.connector.send_client_info("")
         logger.info("Dark image acquisition complete.")
 
-    def acquire_flat(self, num_images: int, exposure_time: float, name="flat"):
+    def acquire_flat(self, num_images: int, exposure_time: float, name="flat", restart=True):
         """
         Acquire flat images.
 
@@ -127,20 +144,23 @@ class TomoComponents:
         logger.info(f"Acquiring {num_images} flat images with exposure time {exposure_time}s.")
         self.connector.send_client_info(f"Acquiring {num_images} flat images.")
 
-        yield from self.restart_cameras(
-            name=name, prefix=name, num_images=num_images, frames_per_trigger=num_images
-        )
+        if restart:
+            yield from self.restart_cameras(
+                name=name, prefix=name, num_images=num_images, frames_per_trigger=num_images
+            )
         # yield from self.open_shutter()
         yield from self.stubs.trigger(min_wait=exposure_time)
         yield from self.complete()
         yield from self.update_live_processing_references(ref_type="flat")
-        yield from self.restore_configs(name=name)
+
+        if restart:
+            yield from self.restore_configs(name=name)
         logger.info("Flat image acquisition complete.")
         self.connector.send_client_info("")
 
-    def acquire_references(self, num_darks: int, num_flats: int, exp_time: float, name: str):
-        yield from self.acquire_dark(num_darks, exposure_time=exp_time, name=name)
-        yield from self.acquire_flat(num_flats, exposure_time=exp_time, name=name)
+    def acquire_references(self, num_darks: int, num_flats: int, exp_time: float, restart=True):
+        yield from self.acquire_dark(num_darks, exposure_time=exp_time, restart=restart)
+        yield from self.acquire_flat(num_flats, exposure_time=exp_time, restart=restart)
 
 
 class AcquireDark(ScanBase):
@@ -152,8 +172,7 @@ class AcquireDark(ScanBase):
 
         Args:
             num_images (int): Number of dark images to acquire.
-            exposure_time (float): Exposure time for each dark image in seconds.
-            name (str): Name for the dark image acquisition. Default: "dark"
+            exp_time (float): Exposure time for each dark image in seconds.
 
         Returns:
             ScanReport
@@ -162,23 +181,59 @@ class AcquireDark(ScanBase):
         self.components = TomoComponents(self)
 
     def scan_report_instructions(self):
-        """
-        Generate scan report instructions for the dark image acquisition.
-        This method provides the necessary instructions to listen to the camera progress during the scan.
-        """
-        if not self.components.cameras:
-            yield from super().scan_report_instructions()
-            return
-
-        # Use the first camera or "gfcam" if available for reporting
-        report_camera = (
-            "gfcam" if "gfcam" in self.components.cameras else self.components.cameras[0]
-        )
-        yield from self.stubs.scan_report_instruction({"device_progress": [report_camera]})
+        yield from self.components.scan_report_instructions()
 
     def scan_core(self):
-        yield from self.components.acquire_dark(self.frames_per_trigger, self.exp_time, name="dark")
+        yield from self.components.acquire_dark(self.frames_per_trigger, self.exp_time, restart=False)
 
+class AcquireFlat(ScanBase):
+    scan_name = "acquire_flat"
+
+    def __init__(self, exp_time: float, frames_per_trigger: int = 1, **kwargs):
+        """
+        Acquire flat images.
+
+        Args:
+            num_images (int): Number of flat images to acquire.
+            exp_time (float): Exposure time for each flat image in seconds.
+
+        Returns:
+            ScanReport
+        """
+        super().__init__(frames_per_trigger=frames_per_trigger, exp_time=exp_time, **kwargs)
+        self.components = TomoComponents(self)
+
+    def scan_report_instructions(self):
+        yield from self.components.scan_report_instructions()
+
+    def scan_core(self):
+        yield from self.components.acquire_flat(self.frames_per_trigger, self.exp_time, restart=False)
+
+class AcquireReferences(ScanBase):
+    scan_name = "acquire_refs"
+
+    def __init__(self, num_darks:int, num_flats:int, exp_time: float, frames_per_trigger: int = 1, **kwargs):
+        """
+        Acquire flats and darks. 
+
+        Args:
+            num_darks (int): Number of dark images to acquire.
+            num_flats (int): Number of flat images to acquire.
+            exp_time (float): Exposure time for each flat image in seconds.
+
+        Returns:
+            ScanReport
+        """
+        super().__init__(frames_per_trigger=frames_per_trigger, exp_time=exp_time, **kwargs)
+        self.num_darks = num_darks
+        self.num_flats = num_flats
+        self.components = TomoComponents(self)
+
+    def scan_report_instructions(self):
+        yield from self.components.scan_report_instructions()
+
+    def scan_core(self):
+        yield from self.components.acquire_references(self.num_darks, self.num_flats, self.frames_per_trigger, self.exp_time, restart=False)
 
 class TomoScan(LineScan):
     scan_name = "tomo_line_scan"
-- 
2.49.1


From e11fb31386a4dd3f16fccb58162ee3b47ef85f22 Mon Sep 17 00:00:00 2001
From: wakonig_k <klaus.wakonig@psi.ch>
Date: Mon, 16 Jun 2025 22:36:00 +0200
Subject: [PATCH 04/10] wip

---
 tomcat_bec/scans/simple_scans.py | 64 ++++++++++++++++++++++++--------
 1 file changed, 48 insertions(+), 16 deletions(-)

diff --git a/tomcat_bec/scans/simple_scans.py b/tomcat_bec/scans/simple_scans.py
index 96a758a..7344d0e 100644
--- a/tomcat_bec/scans/simple_scans.py
+++ b/tomcat_bec/scans/simple_scans.py
@@ -49,6 +49,16 @@ class TomoComponents:
         file_path: str = "",
         frames_per_trigger: int = 1,
     ):
+        """
+        Restart the cameras with a new configuration.
+        This is typically used to reset the cameras during another scan, e.g. before acquiring dark or flat images.
+        Args:
+            name (str): Name of the configuration to restart with.
+            num_images (int): Number of images to acquire.
+            prefix (str): Prefix for the file names.
+            file_path (str): Path where the files will be saved.
+            frames_per_trigger (int): Number of frames to acquire per trigger.
+        """
         if not prefix:
             return
         for cam in self.cameras:
@@ -64,24 +74,32 @@ class TomoComponents:
 
     def scan_report_instructions(self):
         """
-        Generate scan report instructions for the dark image acquisition.
+        Generate scan report instructions for the acquisition.
         This method provides the necessary instructions to listen to the camera progress during the scan.
         """
-        if not self.components.cameras:
-            yield from super().scan_report_instructions()
+        if not self.cameras:
             return
 
         # Use the first camera or "gfcam" if available for reporting
-        report_camera = (
-            "gfcam" if "gfcam" in self.components.cameras else self.components.cameras[0]
-        )
+        report_camera = "gfcam" if "gfcam" in self.cameras else self.cameras[0]
         yield from self.stubs.scan_report_instruction({"device_progress": [report_camera]})
 
     def complete(self):
+        """
+        Complete the acquisition by sending an RPC to each camera.
+        This method is typically called after the acquisition is done to finalize the process and start
+        writing the virtual dataset.
+        """
         for cam in self.cameras:
             yield from self.stubs.send_rpc_and_wait(device=cam, func_name="on_complete")
 
     def restore_configs(self, name: str):
+        """
+        Restore the camera configurations after an acquisition.
+
+        Args:
+            name (str): Name of the configuration to restore.
+        """
         for cam in self.cameras:
             yield from self.stubs.send_rpc_and_wait(
                 device=cam, func_name="restore_config", name=name
@@ -121,7 +139,7 @@ class TomoComponents:
                 name=name, prefix=name, num_images=num_images, frames_per_trigger=num_images
             )
         # yield from self.close_shutter()
-        yield from self.stubs.trigger(min_wait=exposure_time)
+        yield from self.stubs.trigger(min_wait=exposure_time * num_images)
         yield from self.complete()
         yield from self.update_live_processing_references(ref_type="dark")
         if restart:
@@ -149,7 +167,7 @@ class TomoComponents:
                 name=name, prefix=name, num_images=num_images, frames_per_trigger=num_images
             )
         # yield from self.open_shutter()
-        yield from self.stubs.trigger(min_wait=exposure_time)
+        yield from self.stubs.trigger(min_wait=exposure_time * num_images)
         yield from self.complete()
         yield from self.update_live_processing_references(ref_type="flat")
 
@@ -165,8 +183,9 @@ class TomoComponents:
 
 class AcquireDark(ScanBase):
     scan_name = "acquire_dark"
+    gui_config = {"Acquisition Parameters": ["num_images", "exp_time"]}
 
-    def __init__(self, exp_time: float, frames_per_trigger: int = 1, **kwargs):
+    def __init__(self, num_images: int, exp_time: float, **kwargs):
         """
         Acquire dark images.
 
@@ -177,6 +196,7 @@ class AcquireDark(ScanBase):
         Returns:
             ScanReport
         """
+        frames_per_trigger = num_images if num_images > 0 else 1
         super().__init__(frames_per_trigger=frames_per_trigger, exp_time=exp_time, **kwargs)
         self.components = TomoComponents(self)
 
@@ -184,22 +204,28 @@ class AcquireDark(ScanBase):
         yield from self.components.scan_report_instructions()
 
     def scan_core(self):
-        yield from self.components.acquire_dark(self.frames_per_trigger, self.exp_time, restart=False)
+        yield from self.components.acquire_dark(
+            self.frames_per_trigger, self.exp_time, restart=False
+        )
+
 
 class AcquireFlat(ScanBase):
     scan_name = "acquire_flat"
+    gui_config = {"Acquisition Parameters": ["num_images", "exp_time"]}
 
-    def __init__(self, exp_time: float, frames_per_trigger: int = 1, **kwargs):
+    def __init__(self, num_images: int, exp_time: float, **kwargs):
         """
         Acquire flat images.
 
         Args:
             num_images (int): Number of flat images to acquire.
             exp_time (float): Exposure time for each flat image in seconds.
+            frames_per_trigger (int): Number of frames to acquire per trigger.
 
         Returns:
             ScanReport
         """
+        frames_per_trigger = num_images if num_images > 0 else 1
         super().__init__(frames_per_trigger=frames_per_trigger, exp_time=exp_time, **kwargs)
         self.components = TomoComponents(self)
 
@@ -207,24 +233,29 @@ class AcquireFlat(ScanBase):
         yield from self.components.scan_report_instructions()
 
     def scan_core(self):
-        yield from self.components.acquire_flat(self.frames_per_trigger, self.exp_time, restart=False)
+        yield from self.components.acquire_flat(
+            self.frames_per_trigger, self.exp_time, restart=False
+        )
+
 
 class AcquireReferences(ScanBase):
     scan_name = "acquire_refs"
+    gui_config = {"Acquisition Parameters": ["num_darks", "num_flats", "exp_time"]}
 
-    def __init__(self, num_darks:int, num_flats:int, exp_time: float, frames_per_trigger: int = 1, **kwargs):
+    def __init__(self, num_darks: int, num_flats: int, exp_time: float, **kwargs):
         """
-        Acquire flats and darks. 
+        Acquire flats and darks.
 
         Args:
             num_darks (int): Number of dark images to acquire.
             num_flats (int): Number of flat images to acquire.
             exp_time (float): Exposure time for each flat image in seconds.
+            frames_per_trigger (int): Number of frames to acquire per trigger.
 
         Returns:
             ScanReport
         """
-        super().__init__(frames_per_trigger=frames_per_trigger, exp_time=exp_time, **kwargs)
+        super().__init__(exp_time=exp_time, **kwargs)
         self.num_darks = num_darks
         self.num_flats = num_flats
         self.components = TomoComponents(self)
@@ -233,7 +264,8 @@ class AcquireReferences(ScanBase):
         yield from self.components.scan_report_instructions()
 
     def scan_core(self):
-        yield from self.components.acquire_references(self.num_darks, self.num_flats, self.frames_per_trigger, self.exp_time, restart=False)
+        yield from self.components.acquire_references(self.num_darks, self.num_flats, self.exp_time)
+
 
 class TomoScan(LineScan):
     scan_name = "tomo_line_scan"
-- 
2.49.1


From 11251841c3b56a0fc39d0fd27430fffb73eb1f80 Mon Sep 17 00:00:00 2001
From: wakonig_k <klaus.wakonig@psi.ch>
Date: Mon, 16 Jun 2025 22:39:58 +0200
Subject: [PATCH 05/10] wip

---
 tomcat_bec/scans/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tomcat_bec/scans/__init__.py b/tomcat_bec/scans/__init__.py
index fdb7f1f..46e6b20 100644
--- a/tomcat_bec/scans/__init__.py
+++ b/tomcat_bec/scans/__init__.py
@@ -1,5 +1,6 @@
-from .simple_scans import TomoFlyScan, TomoScan, AcquireDark
+from .simple_scans import AcquireDark, AcquireFlat, AcquireReferences, TomoFlyScan, TomoScan
 from .tomcat_scans import TomcatSimpleSequence, TomcatSnapNStep
+
 # from .tutorial_fly_scan import (
 #     # AcquireDark,
 #     AcquireProjections,
-- 
2.49.1


From ab57c482506965d3b0630e0ca8167c44af63d8fe Mon Sep 17 00:00:00 2001
From: gac-x02da <gac-x02da@x02da-bec-001.psi.ch>
Date: Tue, 17 Jun 2025 10:35:29 +0200
Subject: [PATCH 06/10] wip

---
 tomcat_bec/devices/pco_edge/pcoedgecamera.py | 13 ++++++--
 tomcat_bec/scans/simple_scans.py             | 31 ++++++++++----------
 2 files changed, 26 insertions(+), 18 deletions(-)

diff --git a/tomcat_bec/devices/pco_edge/pcoedgecamera.py b/tomcat_bec/devices/pco_edge/pcoedgecamera.py
index 2bc810e..417ffad 100644
--- a/tomcat_bec/devices/pco_edge/pcoedgecamera.py
+++ b/tomcat_bec/devices/pco_edge/pcoedgecamera.py
@@ -245,7 +245,8 @@ class PcoEdge5M(PSIDeviceBase, PcoEdgeBase):
         self,
         name: str,
         file_path: str = "",
-        file_prefix: str = "",
+        file_name: str | None = None,
+        file_suffix:str = "",
         num_images: int | None = None,
         frames_per_trigger: int | None = None,
     ) -> StatusBase:
@@ -263,14 +264,20 @@ class PcoEdge5M(PSIDeviceBase, PcoEdgeBase):
         Returns:
             DeviceStatus: The status of the restart operation. It resolves when the camera is ready to receive the first image.
         """
+        if file_name is not None and file_suffix:
+            raise ValueError("Both file_name and file_suffix are specified. Please choose one.")
+        
         self.acq_configs[name] = {}
         conf = {}
         if file_path:
             self.acq_configs[name]["file_path"] = self.file_path.get()
             conf["file_path"] = file_path
-        if file_prefix:
+        if file_suffix:
             self.acq_configs[name]["file_prefix"] = self.file_prefix.get()
-            conf["file_prefix"] = file_prefix
+            conf["file_prefix"] = "_".join([self.file_prefix.get(), file_suffix])
+        if file_name:
+            self.acq_configs[name]["file_prefix"] = self.file_prefix.get()
+            conf["file_prefix"] = file_name
         if num_images is not None:
             self.acq_configs[name]["num_images"] = self.num_images.get()
             conf["num_images"] = num_images
diff --git a/tomcat_bec/scans/simple_scans.py b/tomcat_bec/scans/simple_scans.py
index 7344d0e..432278f 100644
--- a/tomcat_bec/scans/simple_scans.py
+++ b/tomcat_bec/scans/simple_scans.py
@@ -45,7 +45,7 @@ class TomoComponents:
         self,
         name: str,
         num_images: int,
-        prefix: str = "",
+        file_suffix: str = "",
         file_path: str = "",
         frames_per_trigger: int = 1,
     ):
@@ -55,18 +55,16 @@ class TomoComponents:
         Args:
             name (str): Name of the configuration to restart with.
             num_images (int): Number of images to acquire.
-            prefix (str): Prefix for the file names.
+            file_suffix (str): Suffix for the file names.
             file_path (str): Path where the files will be saved.
             frames_per_trigger (int): Number of frames to acquire per trigger.
         """
-        if not prefix:
-            return
         for cam in self.cameras:
             yield from self.stubs.send_rpc_and_wait(
                 device=cam,
                 func_name="restart_with_new_config",
                 name=name,
-                file_prefix=prefix,
+                file_suffix=file_suffix,
                 file_path=file_path,
                 num_images=num_images,
                 frames_per_trigger=frames_per_trigger,
@@ -121,7 +119,7 @@ class TomoComponents:
                 device=cam, func_name="update_live_processing_reference", reference_type=ref_type
             )
 
-    def acquire_dark(self, num_images: int, exposure_time: float, name="dark", restart=True):
+    def acquire_dark(self, num_images: int, exposure_time: float, name="dark", restart=True, restore=True):
         """
         Acquire dark images.
 
@@ -136,20 +134,20 @@ class TomoComponents:
 
         if restart:
             yield from self.restart_cameras(
-                name=name, prefix=name, num_images=num_images, frames_per_trigger=num_images
+                name=name, file_suffix=name, num_images=num_images, frames_per_trigger=num_images
             )
         # yield from self.close_shutter()
         yield from self.stubs.trigger(min_wait=exposure_time * num_images)
         yield from self.complete()
         yield from self.update_live_processing_references(ref_type="dark")
-        if restart:
+        if restore:
             yield from self.restore_configs(name=name)
 
         # yield from self.open_shutter()
         self.connector.send_client_info("")
         logger.info("Dark image acquisition complete.")
 
-    def acquire_flat(self, num_images: int, exposure_time: float, name="flat", restart=True):
+    def acquire_flat(self, num_images: int, exposure_time: float, name="flat", restart=True, restore=True):
         """
         Acquire flat images.
 
@@ -164,21 +162,21 @@ class TomoComponents:
 
         if restart:
             yield from self.restart_cameras(
-                name=name, prefix=name, num_images=num_images, frames_per_trigger=num_images
+                name=name, file_suffix=name, num_images=num_images, frames_per_trigger=num_images
             )
         # yield from self.open_shutter()
         yield from self.stubs.trigger(min_wait=exposure_time * num_images)
         yield from self.complete()
         yield from self.update_live_processing_references(ref_type="flat")
 
-        if restart:
+        if restore:
             yield from self.restore_configs(name=name)
         logger.info("Flat image acquisition complete.")
         self.connector.send_client_info("")
 
-    def acquire_references(self, num_darks: int, num_flats: int, exp_time: float, restart=True):
-        yield from self.acquire_dark(num_darks, exposure_time=exp_time, restart=restart)
-        yield from self.acquire_flat(num_flats, exposure_time=exp_time, restart=restart)
+    def acquire_references(self, num_darks: int, num_flats: int, exp_time: float, restart=True, restore=True):
+        yield from self.acquire_dark(num_darks, exposure_time=exp_time, restart=restart, restore=restore)
+        yield from self.acquire_flat(num_flats, exposure_time=exp_time, restart=restart, restore=restore)
 
 
 class AcquireDark(ScanBase):
@@ -263,8 +261,11 @@ class AcquireReferences(ScanBase):
     def scan_report_instructions(self):
         yield from self.components.scan_report_instructions()
 
+    def pre_scan(self):
+        yield from self.components.acquire_references(self.num_darks, self.num_flats, self.exp_time, restart=True, restore=False)
+        
     def scan_core(self):
-        yield from self.components.acquire_references(self.num_darks, self.num_flats, self.exp_time)
+        pass
 
 
 class TomoScan(LineScan):
-- 
2.49.1


From 058de83fbed767b9677ebb3f7f9ba2830210288a Mon Sep 17 00:00:00 2001
From: wakonig_k <klaus.wakonig@psi.ch>
Date: Tue, 17 Jun 2025 10:38:29 +0200
Subject: [PATCH 07/10] wip

---
 tomcat_bec/devices/pco_edge/pcoedgecamera.py | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/tomcat_bec/devices/pco_edge/pcoedgecamera.py b/tomcat_bec/devices/pco_edge/pcoedgecamera.py
index 417ffad..1900536 100644
--- a/tomcat_bec/devices/pco_edge/pcoedgecamera.py
+++ b/tomcat_bec/devices/pco_edge/pcoedgecamera.py
@@ -70,6 +70,12 @@ class PcoEdge5M(PSIDeviceBase, PcoEdgeBase):
     analysis_signal = Cpt(Signal, name="analysis_signal", kind=Kind.hinted, doc="Analysis Signal")
     analysis_signal2 = Cpt(Signal, name="analysis_signal2", kind=Kind.hinted, doc="Analysis Signal")
     preview = Cpt(PreviewSignal, ndim=2, name="preview", doc="Camera raw data preview signal")
+    preview_corrected = Cpt(
+        PreviewSignal,
+        ndim=2,
+        name="preview_corrected",
+        doc="Camera preview signal with flat and dark correction",
+    )
     progress = Cpt(
         ProgressSignal,
         name="progress",
@@ -207,8 +213,8 @@ class PcoEdge5M(PSIDeviceBase, PcoEdgeBase):
     def _on_preview_update(self, img: np.ndarray):
         corrected_img = self.live_processing.apply_flat_dark_correction(img)
         self.live_processing.on_new_data(corrected_img)
-        self.preview.put(corrected_img)
-        self._run_subs(sub_type=self.SUB_DEVICE_MONITOR_2D, obj=self, value=corrected_img)
+        self.preview.put(img)
+        self.preview_corrected.put(corrected_img)
 
     def _on_count_update(self, count: int):
         """
@@ -246,7 +252,7 @@ class PcoEdge5M(PSIDeviceBase, PcoEdgeBase):
         name: str,
         file_path: str = "",
         file_name: str | None = None,
-        file_suffix:str = "",
+        file_suffix: str = "",
         num_images: int | None = None,
         frames_per_trigger: int | None = None,
     ) -> StatusBase:
@@ -266,7 +272,7 @@ class PcoEdge5M(PSIDeviceBase, PcoEdgeBase):
         """
         if file_name is not None and file_suffix:
             raise ValueError("Both file_name and file_suffix are specified. Please choose one.")
-        
+
         self.acq_configs[name] = {}
         conf = {}
         if file_path:
@@ -376,7 +382,9 @@ class PcoEdge5M(PSIDeviceBase, PcoEdgeBase):
         status = DeviceStatus(self)
         if self.backend.status != StdDaqStatus.IDLE:
             self.backend.add_status_callback(
-                status, success=[StdDaqStatus.IDLE], error=[StdDaqStatus.REJECTED, StdDaqStatus.ERROR]
+                status,
+                success=[StdDaqStatus.IDLE],
+                error=[StdDaqStatus.REJECTED, StdDaqStatus.ERROR],
             )
             self.backend.stop()
         else:
-- 
2.49.1


From 5699363acf848c08cb9dfa890c7cb99f1c521534 Mon Sep 17 00:00:00 2001
From: wakonig_k <klaus.wakonig@psi.ch>
Date: Tue, 17 Jun 2025 11:01:53 +0200
Subject: [PATCH 08/10] wip

---
 tomcat_bec/devices/pco_edge/pcoedgecamera.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/tomcat_bec/devices/pco_edge/pcoedgecamera.py b/tomcat_bec/devices/pco_edge/pcoedgecamera.py
index 1900536..abc5798 100644
--- a/tomcat_bec/devices/pco_edge/pcoedgecamera.py
+++ b/tomcat_bec/devices/pco_edge/pcoedgecamera.py
@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import os
+from collections import deque
 from typing import TYPE_CHECKING, Literal, cast
 
 import numpy as np
@@ -123,6 +124,7 @@ class PcoEdge5M(PSIDeviceBase, PcoEdgeBase):
         self.backend = StdDaqClient(parent=self, ws_url=std_daq_ws, rest_url=std_daq_rest)
         self.backend.add_count_callback(self._on_count_update)
         self.live_preview = None
+        self.converted_files = deque(maxlen=100)  # Store the last 10 converted files
         self.acq_configs = {}
         if std_daq_live is not None:
             self.live_preview = StdDaqPreview(url=std_daq_live, cb=self._on_preview_update)
@@ -539,6 +541,12 @@ class PcoEdge5M(PSIDeviceBase, PcoEdgeBase):
         """Called to inquire if a device has completed a scans."""
 
         def _create_dataset(_status: DeviceStatus):
+            if self.target_file in self.converted_files:
+                logger.info(
+                    f"File {self.target_file} already exists in the converted files list. "
+                    "Skipping dataset creation."
+                )
+                return
             self.backend.create_virtual_datasets(
                 self.file_path.get(), file_prefix=self.file_prefix.get()  # type: ignore
             )
@@ -547,8 +555,9 @@ class PcoEdge5M(PSIDeviceBase, PcoEdgeBase):
                 file_path=self.target_file,
                 done=True,
                 successful=True,
-                hinted_location={"data": "data"},
+                hinted_location={"data": "tomcat-pco/data"},
             )
+            self.converted_files.append(self.target_file)
             logger.info(f"Finished writing to {self.target_file}")
 
         status = self.acq_done()
-- 
2.49.1


From da9004b4873883a1a377ffd2b146f5cacf0bbab7 Mon Sep 17 00:00:00 2001
From: wakonig_k <klaus.wakonig@psi.ch>
Date: Tue, 17 Jun 2025 11:08:10 +0200
Subject: [PATCH 09/10] wip

---
 tomcat_bec/devices/pco_edge/pcoedgecamera.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/tomcat_bec/devices/pco_edge/pcoedgecamera.py b/tomcat_bec/devices/pco_edge/pcoedgecamera.py
index abc5798..b80faaa 100644
--- a/tomcat_bec/devices/pco_edge/pcoedgecamera.py
+++ b/tomcat_bec/devices/pco_edge/pcoedgecamera.py
@@ -125,6 +125,7 @@ class PcoEdge5M(PSIDeviceBase, PcoEdgeBase):
         self.backend.add_count_callback(self._on_count_update)
         self.live_preview = None
         self.converted_files = deque(maxlen=100)  # Store the last 10 converted files
+        self.target_files = deque(maxlen=100)  # Store the last 10 target files
         self.acq_configs = {}
         if std_daq_live is not None:
             self.live_preview = StdDaqPreview(url=std_daq_live, cb=self._on_preview_update)
@@ -361,6 +362,7 @@ class PcoEdge5M(PSIDeviceBase, PcoEdgeBase):
             num_images=self.num_images.get(),  # type: ignore
         )
         self.camera_status.set(CameraStatus.RUNNING).wait()
+        self.target_files.append(self.target_file)
 
         def is_running(*, value, timestamp, **_):
             return bool(value == CameraStatusCode.RUNNING)
@@ -541,11 +543,11 @@ class PcoEdge5M(PSIDeviceBase, PcoEdgeBase):
         """Called to inquire if a device has completed a scans."""
 
         def _create_dataset(_status: DeviceStatus):
-            if self.target_file in self.converted_files:
-                logger.info(
-                    f"File {self.target_file} already exists in the converted files list. "
-                    "Skipping dataset creation."
-                )
+            if (
+                self.target_file in self.converted_files
+                or self.target_file not in self.target_files
+            ):
+                logger.info(f"File {self.target_file} already processed or not in target files.")
                 return
             self.backend.create_virtual_datasets(
                 self.file_path.get(), file_prefix=self.file_prefix.get()  # type: ignore
-- 
2.49.1


From 26c52e21bea485efc011b5741f67e7289b065db9 Mon Sep 17 00:00:00 2001
From: gac-x02da <gac-x02da@x02da-bec-001.psi.ch>
Date: Wed, 18 Jun 2025 15:25:30 +0200
Subject: [PATCH 10/10] wip

---
 tomcat_bec/devices/pco_edge/pcoedgecamera.py          | 3 ++-
 tomcat_bec/devices/std_daq/std_daq_live_processing.py | 2 +-
 tomcat_bec/scans/simple_scans.py                      | 6 +++---
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/tomcat_bec/devices/pco_edge/pcoedgecamera.py b/tomcat_bec/devices/pco_edge/pcoedgecamera.py
index b80faaa..aad85f7 100644
--- a/tomcat_bec/devices/pco_edge/pcoedgecamera.py
+++ b/tomcat_bec/devices/pco_edge/pcoedgecamera.py
@@ -70,12 +70,13 @@ class PcoEdge5M(PSIDeviceBase, PcoEdgeBase):
 
     analysis_signal = Cpt(Signal, name="analysis_signal", kind=Kind.hinted, doc="Analysis Signal")
     analysis_signal2 = Cpt(Signal, name="analysis_signal2", kind=Kind.hinted, doc="Analysis Signal")
-    preview = Cpt(PreviewSignal, ndim=2, name="preview", doc="Camera raw data preview signal")
+    preview = Cpt(PreviewSignal, ndim=2, name="preview", doc="Camera raw data preview signal", num_rotation_90=1, transpose=False)
     preview_corrected = Cpt(
         PreviewSignal,
         ndim=2,
         name="preview_corrected",
         doc="Camera preview signal with flat and dark correction",
+        num_rotation_90=1, transpose=False
     )
     progress = Cpt(
         ProgressSignal,
diff --git a/tomcat_bec/devices/std_daq/std_daq_live_processing.py b/tomcat_bec/devices/std_daq/std_daq_live_processing.py
index 714c5ea..5368d24 100644
--- a/tomcat_bec/devices/std_daq/std_daq_live_processing.py
+++ b/tomcat_bec/devices/std_daq/std_daq_live_processing.py
@@ -126,7 +126,7 @@ class StdDaqLiveProcessing:
         corrected_data = np.divide(
             data - dark, flat_corr, out=np.zeros_like(data, dtype=np.float32), where=flat_corr != 0
         )
-        return corrected_data
+        return np.clip(corrected_data, a_min=0, a_max=None)
 
     @typechecked
     def _load_and_update_reference(
diff --git a/tomcat_bec/scans/simple_scans.py b/tomcat_bec/scans/simple_scans.py
index 432278f..8419ee6 100644
--- a/tomcat_bec/scans/simple_scans.py
+++ b/tomcat_bec/scans/simple_scans.py
@@ -262,11 +262,11 @@ class AcquireReferences(ScanBase):
         yield from self.components.scan_report_instructions()
 
     def pre_scan(self):
-        yield from self.components.acquire_references(self.num_darks, self.num_flats, self.exp_time, restart=True, restore=False)
+        yield from self.components.acquire_references(self.num_darks, self.num_flats, self.exp_time)
         
     def scan_core(self):
-        pass
-
+        yield None
+    
 
 class TomoScan(LineScan):
     scan_name = "tomo_line_scan"
-- 
2.49.1