variables for progress

csaxs_bec/bec_ipython_client/plugins/LamNI/x_ray_eye_align.py

@@ -525,6 +525,7 @@ class LamNI(LamNIOpticsMixin):
         self._beam_is_okay = True
         self._stop_beam_check_event = None
         self.beam_check_thread = None
+        self.progress = {}
 
     def get_beamline_checks_enabled(self):
         print(
@@ -587,6 +588,27 @@ class LamNI(LamNIOpticsMixin):
     def tomo_circfov(self, val: float):
         self.client.set_global_var("tomo_circfov", val)
 
+    @property
+    def tomo_type(self):
+        val = self.client.get_global_var("tomo_type")
+        if val is None:
+            return 1
+        return val
+
+    @tomo_type.setter
+    def tomo_type(self, val: float):
+        if val == 1:
+            # equally spaced tomography with 8 sub tomograms
+            self.client.set_global_var("tomo_type", val)
+        #elif val == 2:
+        #    # golden ratio tomography (sorted bunches)
+        #    self.client.set_global_var("tomo_type", val)
+        #elif val == 3:
+        #    # equally spaced tomography with starting angles shifted by golden ratio
+        #    self.client.set_global_var("tomo_type", val)
+        else:
+            raise ValueError("Unknown tomo_type.")
+
     @property
     def tomo_countingtime(self):
         val = self.client.get_global_var("tomo_countingtime")
@@ -949,47 +971,73 @@ class LamNI(LamNIOpticsMixin):
         # _tomo_shift_angles (potential global variable)
         _tomo_shift_angles = 0
         angle_end = start_angle + 360
-        for angle in np.linspace(
+        angles = np.linspace(
             start_angle + _tomo_shift_angles,
             angle_end,
             num=int(360 / self.tomo_angle_stepsize) + 1,
             endpoint=True,
-        ):
-            successful = False
-            error_caught = False
-            if 0 <= angle < 360.05:
-                print(f"Starting LamNI scan for angle {angle}")
-                while not successful:
-                    self._start_beam_check()
-                    if not self.special_angles:
-                        self._current_special_angles = []
-                    if self._current_special_angles:
-                        next_special_angle = self._current_special_angles[0]
-                        if np.isclose(angle, next_special_angle, atol=0.5):
-                            self._current_special_angles.pop(0)
-                            num_repeats = self.special_angle_repeats
-                    else:
-                        num_repeats = 1
-                    try:
-                        start_scan_number = bec.queue.next_scan_number
-                        for i in range(num_repeats):
-                            self._at_each_angle(angle)
-                        error_caught = False
-                    except AlarmBase as exc:
-                        if exc.alarm_type == "TimeoutError":
-                            bec.queue.request_queue_reset()
-                            time.sleep(2)
-                            error_caught = True
-                        else:
-                            raise exc
+        )
+        # reverse even sub-tomograms
+        if not (subtomo_number % 2):
+            angles = np.flip(angles)
+        for angle in angles:
+            self.progress["subtomo"] = subtomo_number
+            self.progress["subtomo_projection"] = angles.index(angle)
+            self.progress["subtomo_total_projections"] = 180 / self.tomo_angle_stepsize
+            self.progress["projection"] = (subtomo_number - 1) * self.progress[
+                "subtomo_total_projections"
+            ] + self.progress["subtomo_projection"]
+            self.progress["total_projections"] = 180 / self.tomo_angle_stepsize * 8
+            self.progress["angle"] = angle
+            self._tomo_scan_at_angle(angle, subtomo_number)
 
-                    if self._was_beam_okay() and not error_caught:
-                        successful = True
+    def _print_progress(self):
+        print("\x1b[95mProgress report:")
+        print(f"Tomo type: ....................... {self.progress['tomo_type']}")
+        print(f"Projection: ...................... {self.progress['projection']}")
+        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")
+
+
+    def _tomo_scan_at_angle(self, angle, subtomo_number):
+        successful = False
+        error_caught = False
+        if 0 <= angle < 360.05:
+            print(f"Starting LamNI scan for angle {angle} in subtomo {subtomo_number}")
+            self._print_progress()
+            while not successful:
+                self._start_beam_check()
+                if not self.special_angles:
+                    self._current_special_angles = []
+                if self._current_special_angles:
+                    next_special_angle = self._current_special_angles[0]
+                    if np.isclose(angle, next_special_angle, atol=0.5):
+                        self._current_special_angles.pop(0)
+                        num_repeats = self.special_angle_repeats
+                else:
+                    num_repeats = 1
+                try:
+                    start_scan_number = bec.queue.next_scan_number
+                    for i in range(num_repeats):
+                        self._at_each_angle(angle)
+                    error_caught = False
+                except AlarmBase as exc:
+                    if exc.alarm_type == "TimeoutError":
+                        bec.queue.request_queue_reset()
+                        time.sleep(2)
+                        error_caught = True
                     else:
-                        self._wait_for_beamline_checks()
-                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, subtomo_number)
+                        raise exc
+
+                if self._was_beam_okay() and not error_caught:
+                    successful = True
+                else:
+                    self._wait_for_beamline_checks()
+            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, subtomo_number)
 
     def _write_tomo_scan_number(self, scan_number: int, angle: float, subtomo_number: int) -> None:
         tomo_scan_numbers_file = os.path.expanduser(
@@ -1007,22 +1055,29 @@ class LamNI(LamNIOpticsMixin):
         scans = builtins.__dict__.get("scans")
         self._current_special_angles = self.special_angles.copy()
 
-        if subtomo_start == 1 and start_angle is None:
+        if (self.tomo_type == 1 and subtomo_start == 1 and start_angle is None):
             # pylint: disable=undefined-variable
-            self.tomo_id = self.add_sample_database(
-                self.sample_name,
-                str(datetime.date.today()),
-                bec.active_account.decode(),
-                bec.queue.next_scan_number,
-                "lamni",
-                "test additional info",
-                "BEC",
-            )
-            self.write_pdf_report()
+            if bec.active_account != "":
+                self.tomo_id = self.add_sample_database(
+                    self.sample_name,
+                    str(datetime.date.today()),
+                    bec.active_account.decode(),
+                    bec.queue.next_scan_number,
+                    "lamni",
+                    "test additional info",
+                    "BEC",
+                )
+                self.write_pdf_report()
+            else:
+                self.tomo_id = 0
+
         with scans.dataset_id_on_hold:
-            for ii in range(subtomo_start, 9):
-                self.sub_tomo_scan(ii, start_angle=start_angle)
-                start_angle = None
+            if self.tomo_type == 1:
+                # 8 equally spaced sub-tomograms
+                self.progress["tomo_type"] = "Equally spaced sub-tomograms"
+                for ii in range(subtomo_start, 9):
+                    self.sub_tomo_scan(ii, start_angle=start_angle)
+                    start_angle = None
 
     def tomo_parameters(self):
         """print and update the tomo parameters"""
@@ -1045,8 +1100,10 @@ class LamNI(LamNIOpticsMixin):
         print(f"   _tomo_fovy_offset       <mm>  =  {self.align.tomo_fovy_offset}")
         print(f"   _manual_shift_x         <mm>  =  {self.manual_shift_x}")
         print(f"   _manual_shift_y         <mm>  =  {self.manual_shift_y}")
-        print(f"Angular step within sub-tomogram:   {self.tomo_angle_stepsize} degrees")
-        print(f"Resulting in number of projections: {360/self.tomo_angle_stepsize*8}")
+        if self.tomo_type == 1:
+            print("\x1b[1mTomo type 1:\x1b[0m 8 equally spaced sub-tomograms")
+            print(f"Total number of projections: {360/self.tomo_angle_stepsize*8}")
+            print(f"Angular step within sub-tomogram:   {self.tomo_angle_stepsize} degrees")
         print(f"Sample name: {self.sample_name}\n")
 
         user_input = input("Are these parameters correctly set for your scan? ")