diff --git a/maxwell_integrate_to_h5.py b/maxwell_integrate_to_h5.py
index 5976eb6b493599d384070890ba8fca50520ced97..dc5b14caec94065f03f9bc82a847262e667c40f5 100644
--- a/maxwell_integrate_to_h5.py
+++ b/maxwell_integrate_to_h5.py
@@ -136,44 +136,117 @@ def integrate_ims_in_dir(path_im, path_int, dtype_im=".tif", dtype_int=".dat"):
print(f"File {output_file} already exists. Removing it to create a new one.")
os.remove(output_file)
- with h5py.File(output_file, "w") as f:
- # Top-level NXroot
- nxroot = f.create_group(subdir_name)
- nxroot.attrs["NX_class"] = np.string_("NXroot")
- nxroot.attrs["default"] = np.string_("1.1")
+
+ with h5py.File(output_file, "w") as h5:
+ entry = h5.create_group(f"/{subdir_name}")
+ entry.attrs["NX_class"] = "NXentry"
+ entry.attrs["default"] = "last_plot" # reference to the last spectrum
for idx, result in enumerate(results_data, start=1):
- entry_name = f"{idx}.1"
- entry = nxroot.create_group(entry_name)
- entry.attrs["NX_class"] = np.string_("NXentry")
- entry.attrs["default"] = np.string_("plotdata")
-
- # Create full measurement group
- meas = entry.create_group("measurement")
- meas.attrs["NX_class"] = np.string_("NXcollection")
- meas.attrs["filename"] = np.string_(result["filename"])
-
- meas.create_dataset("q", data=result["q"])
- meas.create_dataset("I", data=result["I"])
- meas.create_dataset("dI", data=result["dI"])
-
- # Create plotdata group with proper NXdata spec
- plot = entry.create_group("plotdata")
- plot.attrs["NX_class"] = np.string_("NXdata")
- plot.attrs["signal"] = np.string_("I")
- plot.attrs["axes"] = np.string_("q")
- plot.attrs["title"] = np.string_(result["filename"])
-
- plot.create_dataset("q", data=result["q"])
- dset_I = plot.create_dataset("I", data=result["I"])
- dset_I.attrs["long_name"] = np.string_(result["filename"])
- plot["I"].attrs["long_name"] = "Intensity"
- plot["q"].attrs["long_name"] = "Ang^-1"
-
- plot.create_dataset("dI", data=result["dI"])
- plot["dI"].attrs["long_name"] = np.string_("Uncertainty in I")
+ scan_name = f"{idx:03d}" # e.g., '001'
+ scan_group = entry.create_group(scan_name)
+
+ # Instrument / Detector group
+ detector = scan_group.create_group("instrument/detector")
+ detector.attrs["NX_class"] = "NXdetector"
+ chunk_size = min(len(result["I"]), 1000)
+
+ detector.create_dataset("q", data=np.asarray(result["q"], dtype=np.float64), chunks=(chunk_size,))
+ detector.create_dataset("I", data=np.asarray(result["I"], dtype=np.float64), chunks=(chunk_size,))
+ detector.create_dataset("dI", data=np.asarray(result["dI"], dtype=np.float64), chunks=(chunk_size,))
+
+ # Add interpretation info (optional for PyMca)
+ detector["I"].attrs["interpretation"] = "spectrum"
+
+ # Measurement group (holds soft links)
+ meas = scan_group.create_group("measurement")
+ meas.attrs["NX_class"] = "NXdata"
+ meas.attrs["signal"] = "I"
+ meas.attrs["axes"] = "q"
+ meas.attrs["filename"] = result["filename"]
+
+ meas["I"] = h5py.SoftLink(f"/{subdir_name}/{scan_name}/instrument/detector/I")
+ meas["q"] = h5py.SoftLink(f"/{subdir_name}/{scan_name}/instrument/detector/q")
+ meas["dI"] = h5py.SoftLink(f"/{subdir_name}/{scan_name}/instrument/detector/dI")
+
+ # Optional display-friendly names
+ meas["I"].attrs["long_name"] = "Intensity"
+ meas["q"].attrs["long_name"] = "Q [1/A]"
+
+ # For PyMca auto-plot:
+ scan_group.attrs["default"] = "measurement"
+ # Optional global default plot group
+ if idx == len(results_data): # mark the last one as global default
+ entry["last_plot"] = h5py.SoftLink(f"/{subdir_name}/{scan_name}/measurement")
+ # Title or metadata
+ entry["title"] = "Collected Q-I scans"
+
+ h5.flush()
+
+ # h5 = h5py.File(output_file, "w")
+ # h5["/entry/instrument/q/data"] = result["q"]
+ # h5["/entry/instrument/I/data"] = result["I"]
+ # h5["/entry/instrument/dI/data"] = result["dI"]
+
+ # h5["/entry/title"] = subdir_name
+ # h5["/entry"].attrs["NX_class"] = u"NXentry"
+ # h5["/entry/instrument"].attrs["NX_class"] = u"NXinstrument"
+ # h5["/entry/instrument/q/"].attrs["NX_class"] = u"NXdetector"
+ # h5["/entry/instrument/I/"].attrs["NX_class"] = u"NXdetector"
+ # h5["/entry/instrument/dI/"].attrs["NX_class"] = u"NXdetector"
+
+ # h5["/entry/instrument/q/data"].attrs["interpretation"] = u"Dataset"
+ # h5["/entry/instrument/I/data"].attrs["interpretation"] = u"Dataset"
+ # h5["/entry/instrument/dI/data"].attrs["interpretation"] = u"Dataset"
+
+ # h5["/entry/measurement/q"] = h5py.SoftLink("/entry/instrument/q/data")
+ # h5["/entry/measurement/I"] = h5py.SoftLink("/entry/instrument/I/data")
+ # h5["/entry/measurement/dI"] = h5py.SoftLink("/entry/instrument/dI/data")
+ # h5["/entry/measurement"].attrs["NX_class"] = u"NXcollection"
+ # h5["/entry/measurement"].attrs["signal"] = u"I"
+ # h5["/entry"].attrs["default"] = u"measurement"
+
+ # # Top-level NXroot
+ # nxroot = f.create_group(subdir_name)
+ # nxroot.attrs["NX_class"] = np.string_("NXroot")
+ # nxroot.attrs["default"] = np.string_("1.1")
+
+ # for idx, result in enumerate(results_data, start=1):
+ # entry_name = f"{idx}.1"
+ # entry = nxroot.create_group(entry_name)
+ # entry.attrs["NX_class"] = np.string_("NXentry")
+ # entry.attrs["default"] = np.string_("plotdata")
+
+ # # Create full measurement group
+ # meas = entry.create_group("measurement")
+ # meas.attrs["NX_class"] = np.string_("NXcollection")
+ # meas.attrs["filename"] = np.string_(result["filename"])
+
+ # meas.create_dataset("q", data=result["q"])
+ # meas.create_dataset("I", data=result["I"])
+ # meas.create_dataset("dI", data=result["dI"])
+
+ # # Create plotdata group with proper NXdata spec
+ # plot = entry.create_group("plotdata")
+ # plot.attrs["NX_class"] = np.string_("NXdata")
+ # plot.attrs["signal"] = np.string_("I")
+ # plot.attrs["axes"] = np.string_("q")
+ # plot.attrs["title"] = np.string_(result["filename"])
+
+ # plot.create_dataset("q", data=result["q"])
+ # dset_I = plot.create_dataset("I", data=result["I"])
+ # dset_I.attrs["long_name"] = np.string_(result["filename"])
+ # plot["I"].attrs["long_name"] = "Intensity"
+ # plot["q"].attrs["long_name"] = "Ang^-1"
+
+ # plot.create_dataset("dI", data=result["dI"])
+ # plot["dI"].attrs["long_name"] = np.string_("Uncertainty in I")
+
+
+ h5.flush()
+ h5.close()
print(f"✅ HDF5 file '{output_file}' created with {len(results_data)} spectra.")
# # Sort results_data by filename
# def natural_sort_key(item):