save roi in pixels with images

csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py

@@ -70,14 +70,26 @@ class XrayEyeAlign:
         # so a second submission at step==1 is treated as the real angle-0
         # fit point instead of triggering another height correction.
         self._height_centered = False
+        # Raw pixel coords + ROI size collected at each submit:
+        # [[step_k, x_px, y_px, w_px, h_px, image_idx], ...]
+        # image_idx refers to alignment_images[image_idx], i.e. the last
+        # frame captured before that submit (shutter is closed at submit time).
+        self.roi_pixel_data = []
 
-    def _save_alignment_data(self, file_path: str):
-        os.makedirs(os.path.dirname(file_path), exist_ok=True)
-        with h5py.File(os.path.expanduser(file_path), "w") as f:
+    def _save_alignment_data(self, file_path: str, fit_data: np.ndarray | None = None):
+        expanded = os.path.expanduser(file_path)
+        os.makedirs(os.path.dirname(expanded), exist_ok=True)
+        with h5py.File(expanded, "w") as f:
             f.create_dataset(
                 "alignment_values", data=np.array(list(self.alignment_values.values()))
             )
             f.create_dataset("alignment_images", data=np.array(self.alignment_images))
+            if self.roi_pixel_data:
+                ds = f.create_dataset("roi_pixel_data", data=np.array(self.roi_pixel_data))
+                ds.attrs["columns"] = ["step_k", "x_px", "y_px", "w_px", "h_px", "image_idx"]
+            if fit_data is not None:
+                ds = f.create_dataset("alignment_fit", data=fit_data)
+                ds.attrs["rows"] = ["angles_deg", "offsets_um", "zeros"]
 
     def update_frame(self, keep_shutter_open=False):
         if self.flomni._flomnigui_check_attribute_not_exists("xeyegui"):
@@ -220,6 +232,20 @@ class XrayEyeAlign:
                 # reset submit channel
                 dev.omny_xray_gui.submit.set(0)
 
+                # Raw pixel position and ROI size at submit time.
+                # The relevant image is the last captured frame (shutter is
+                # closed by the time the user clicks submit).
+                _raw_x = getattr(dev.omny_xray_gui, f"xval_x_{k}").get()
+                _raw_y = getattr(dev.omny_xray_gui, f"yval_y_{k}").get()
+                _raw_w = getattr(dev.omny_xray_gui, f"width_x_{k}").get()
+                _raw_h = getattr(dev.omny_xray_gui, f"width_y_{k}").get()
+                _img_idx = len(self.alignment_images) - 1
+                print(
+                    f"  Submit k={k}: px x={_raw_x:.1f} y={_raw_y:.1f} "
+                    f"w={_raw_w:.1f} h={_raw_h:.1f} img={_img_idx}"
+                )
+                self.roi_pixel_data.append([k, _raw_x, _raw_y, _raw_w, _raw_h, _img_idx])
+
                 # Controls whether `k` advances to the next step below. Left
                 # True except for the height-centering submission, which
                 # reuses k==1 for a second, real submission afterwards.
@@ -252,9 +278,8 @@ class XrayEyeAlign:
                     self.gui.show_crosshair()
 
                     self.send_message(
-                                            "Adjust sample height with the arrows if needed, then mark "
-                                            "the sample and submit - height will be centered automatically"
-                                        )
+                        "Submit height. Use arrows if far off."
+                    )
                     self.gui.enable_submit_button(True)
                     self.movement_buttons_enabled(True, True)
 
@@ -373,37 +398,22 @@ class XrayEyeAlign:
         )
 
     def write_output(self):
-        file = os.path.expanduser("~/data/raw/logs/xrayeye_alignmentvalues/xrayeye_alignmentvalues")
         timestamp = time.strftime("%Y%m%d_%H%M%S")
-        self._save_alignment_data(file + f"_image_data_{timestamp}.h5")
-        if not os.path.exists(file):
-            os.makedirs(os.path.dirname(file), exist_ok=True)
+        file_h5 = f"~/data/raw/logs/xrayeye_alignmentvalues/xrayeye_alignmentvalues_{timestamp}.h5"
 
-        with open(file, "w") as alignment_values_file:
-            alignment_values_file.write("angle\thorizontal\n")
+        fovx_offsets = np.zeros(5)
+        for k in range(1, 6):
+            fovx_offset = self.alignment_values[0] - self.alignment_values[k]
+            fovx_offsets[k - 1] = fovx_offset
+            print(f"Alignment number {k}, value x {fovx_offset}")
 
-            # Initialize an empty list to store fovx values
-            fovx_list = []
-            fovx_offsets = np.zeros(5)  # holds offsets for k = 1..5
-
-            for k in range(1, 6):
-                fovx_offset = self.alignment_values[0] - self.alignment_values[k]
-                fovx_offsets[k - 1] = fovx_offset  # store in array
-
-                fovx_x = (k - 1) * 45
-                fovx_list.append([fovx_x, fovx_offset * 1000])  # Append the data to the list
-
-                print(f"Alignment number {k}, value x {fovx_offset}")
-                alignment_values_file.write(f"{fovx_x}\t{fovx_offset * 1000}\n")
-
-            # Now build final numpy array:
-            data = np.array(
-                [
-                    [0, 45, 90, 135, 180],  # angles
-                    fovx_offsets * 1000,  # fovx_offset values
-                    [0, 0, 0, 0, 0],
-                ]
-            )
+        data = np.array(
+            [
+                [0, 45, 90, 135, 180],  # angles
+                fovx_offsets * 1000,  # fovx_offset values
+                [0, 0, 0, 0, 0],
+            ]
+        )
+        self._save_alignment_data(file_h5, fit_data=data)
         self.gui.submit_fit_array(data)
-        print(f"fit submited with {data}")
-        # self.flomni.flomnigui_show_xeyealign_fittab()
+        print(f"fit submited with {data}")