Add save dicoms function

src/osipi/DRO/_utils.py

@@ -0,0 +1,83 @@
+import os
+
+import numpy as np
+import pydicom
+from matplotlib import pyplot as plt
+from matplotlib.animation import FuncAnimation
+
+
+def animate_mri(slices, mode="time", slice_index=0, time_index=0):
+    fig, ax = plt.subplots()
+    if mode == "time":
+        frames = slices.shape[-1]
+
+        def init():
+            ax.imshow(slices[:, :, slice_index, 0], cmap="gray")
+            ax.set_title(f"Slice: {slice_index}, Time: 0")
+
+        def animate(t):
+            ax.clear()
+            ax.imshow(slices[:, :, slice_index, t], cmap="gray")
+            ax.set_title(f"Slice: {slice_index}, Time: {t}")
+
+    elif mode == "slice":
+        frames = slices.shape[2]
+
+        def init():
+            ax.imshow(slices[:, :, 0, time_index], cmap="gray")
+            ax.set_title(f"Slice: 0, Time: {time_index}")
+
+        def animate(z):
+            ax.clear()
+            ax.imshow(slices[:, :, z, time_index], cmap="gray")
+            ax.set_title(f"Slice: {z}, Time: {time_index}")
+
+    anim = FuncAnimation(
+        fig=fig, func=animate, frames=frames, init_func=init, interval=100, blit=False
+    )
+    plt.show()
+    return anim
+
+
+def save_dicoms(outdir, original_dicom, signal, patient_id_num, study_instance_uid):
+    new_dicoms = original_dicom.copy()
+    patient_id_num = "RIDER Neuro MRI-{}".format(patient_id_num)
+
+    uidprefix = "1.3.6.1.4.1.9328.50.16."
+
+    SeriesInstanceUID = pydicom.uid.generate_uid(prefix=uidprefix)
+    StorageMediaFileSetUID = pydicom.uid.generate_uid(prefix=uidprefix)
+    FrameOfReferenceUID = pydicom.uid.generate_uid(prefix=uidprefix)
+    SeriesID = SeriesInstanceUID[-5:]
+    Seriesdir = "{}.000000-perfusion-{}".format(original_dicom[0][0].SeriesNumber, SeriesID)
+    StudyDate = "19040323"
+    DateID = study_instance_uid[-5:]
+    Datedir = "23-03-1904-BRAINRESEARCH-{}".format(DateID)
+
+    if not os.path.exists(outdir):
+        os.makedirs("{}/{}/{}/{}".format(outdir, patient_id_num, Datedir, Seriesdir))
+
+    z = 0
+    for entries in new_dicoms:
+        t = 0
+        for snap in new_dicoms["{}".format(entries)]:
+            SOPInstanceUID = pydicom.uid.generate_uid(prefix=uidprefix)
+            snap.PatientID = patient_id_num
+            snap.SOPInstanceUID = SOPInstanceUID
+            snap.StudyInstanceUID = study_instance_uid
+            snap.SeriesInstanceUID = SeriesInstanceUID
+            snap.StorageMediaFileSetUID = StorageMediaFileSetUID
+            snap.FrameOfReferenceUID = FrameOfReferenceUID
+            snap.StudyDate = StudyDate
+            snap.ContentDate = StudyDate
+            Sout = abs(signal[:, :, z, t])
+            Sout = Sout.astype(np.uint16)
+            snap.PixelData = Sout.tobytes()
+            fname = str(t + 1).zfill(2) + "-" + str(z + 1).zfill(4)
+            snap.save_as(
+                "{}/{}/{}/{}/{}.dcm".format(outdir, patient_id_num, Datedir, Seriesdir, fname),
+                write_like_original=False,
+            )
+            t += 1
+        z += 1
+    return