Merge pull request #387 from FABLE-3DXRD/segmenter-utils

Move SegmenterGui utils into a separate file

ImageD11/nbGui/segmenter_gui.py

@@ -1,81 +1,11 @@
-import os
 import numpy as np
 import matplotlib.pyplot as plt
 from ipywidgets import interact, interactive, widgets, fixed, Layout
 from IPython.display import display
 import h5py
 import ImageD11.sinograms.lima_segmenter
 import ImageD11.sparseframe
-
-
-def guess_ESRF_paths():  # This should be in silx somewhere?
-    """ Locates:
-    dataroot     holds raw data       in folders dataroot     + {sample}/{sample}_{dataset}
-    analysisroot holds output results in folders analysisroot + {sample}/{sample}_{dataset}
-    """
-    path_items = os.getcwd().split('/')
-    if 'visitor' in path_items:
-        idx = path_items.index('visitor')
-        experiment, session = path_items[idx + 1], path_items[idx + 3]
-        path = os.path.join("/data", "visitor", experiment, "id11", session)
-        return [os.path.join(path, folder) for folder in
-                ("RAW_DATA", "PROCESSED_DATA")]
-    return "", ""
-
-
-def printsamples(dataroot):
-    samples = sorted([name for name in os.listdir(dataroot)
-                      if os.path.isdir(os.path.join(dataroot, name))])
-    print("Samples:\n\t " + "\n\t".join(sorted(samples)))
-
-
-def printdatasets(dataroot, sample):
-    sroot = os.path.join(dataroot, sample)
-    print("Datsets:\n\t " + "\n\t".join(sorted(
-        [name[len(sample) + 1:] for name in os.listdir(sroot)
-         if os.path.isdir(os.path.join(sroot, name))
-         and name.startswith(sample)])))
-
-
-def chooseframe(dset, scan=None, idx=None, counter="_roi1", fetch_raw_image=False):
-    """
-    Locate a busy frame from the dataset and optionally fetch the raw image.
-
-    Args:
-        dset: Dataset object.
-        scan: Scan to use (default is middle scan).
-        idx: Frame index (None to auto-detect).
-        counter: Counter to use for locating the frame.
-        fetch_raw_image: Whether to fetch the raw image for the frame.
-
-    Returns:
-        scan, idx, raw_image (if fetch_raw_image is True, otherwise None)
-    """
-    if scan is None:
-        scan = dset.scans[len(dset.scans) // 2]
-
-    raw_image = None
-    with h5py.File(dset.masterfile, "r") as hin:
-        ctr = dset.detector + counter
-
-        if idx is None:
-            if scan.find("::") > -1:  # 1.1::[10000:12000]  etc
-                lo, hi = [int(v) for v in scan[:-1].split("[")[1].split(":")]
-                scan = scan.split("::")[0]
-                roi1 = hin[scan]["measurement"][ctr][lo:hi]
-                idx = np.argmax(roi1) + lo
-            else:  # "1.1"
-                roi1 = hin[scan]["measurement"][ctr][:]
-                idx = np.argmax(roi1)
-
-        print("Using frame", idx, "from scan", scan)
-
-        # placing the raw image
-        if fetch_raw_image:
-            raw_image = hin[scan + "/measurement/" + dset.detector][idx]
-
-    return scan, idx, raw_image
-
+from ImageD11.nbGui.segmenter_gui_utils import * 
 
 class SegmenterGui:
     """ UI for a jupyter notebook to set the segmentation parameters

ImageD11/nbGui/segmenter_gui_utils.py

@@ -0,0 +1,72 @@
+import h5py
+import numpy as np
+import os
+
+
+def guess_ESRF_paths():  # This should be in silx somewhere?
+    """ Locates:
+    dataroot     holds raw data       in folders dataroot     + {sample}/{sample}_{dataset}
+    analysisroot holds output results in folders analysisroot + {sample}/{sample}_{dataset}
+    """
+    path_items = os.getcwd().split('/')
+    if 'visitor' in path_items:
+        idx = path_items.index('visitor')
+        experiment, session = path_items[idx + 1], path_items[idx + 3]
+        path = os.path.join("/data", "visitor", experiment, "id11", session)
+        return [os.path.join(path, folder) for folder in
+                ("RAW_DATA", "PROCESSED_DATA")]
+    return "", ""
+
+
+def printsamples(dataroot):
+    samples = sorted([name for name in os.listdir(dataroot)
+                      if os.path.isdir(os.path.join(dataroot, name))])
+    print("Samples:\n\t " + "\n\t".join(sorted(samples)))
+
+
+def printdatasets(dataroot, sample):
+    sroot = os.path.join(dataroot, sample)
+    print("Datsets:\n\t " + "\n\t".join(sorted(
+        [name[len(sample) + 1:] for name in os.listdir(sroot)
+         if os.path.isdir(os.path.join(sroot, name))
+         and name.startswith(sample)])))
+
+
+def chooseframe(dset, scan=None, idx=None, counter="_roi1", fetch_raw_image=False):
+    """
+    Locate a busy frame from the dataset and optionally fetch the raw image.
+
+    Args:
+        dset: Dataset object.
+        scan: Scan to use (default is middle scan).
+        idx: Frame index (None to auto-detect).
+        counter: Counter to use for locating the frame.
+        fetch_raw_image: Whether to fetch the raw image for the frame.
+
+    Returns:
+        scan, idx, raw_image (if fetch_raw_image is True, otherwise None)
+    """
+    if scan is None:
+        scan = dset.scans[len(dset.scans) // 2]
+
+    raw_image = None
+    with h5py.File(dset.masterfile, "r") as hin:
+        ctr = dset.detector + counter
+
+        if idx is None:
+            if scan.find("::") > -1:  # 1.1::[10000:12000]  etc
+                lo, hi = [int(v) for v in scan[:-1].split("[")[1].split(":")]
+                scan = scan.split("::")[0]
+                roi1 = hin[scan]["measurement"][ctr][lo:hi]
+                idx = np.argmax(roi1) + lo
+            else:  # "1.1"
+                roi1 = hin[scan]["measurement"][ctr][:]
+                idx = np.argmax(roi1)
+
+        print("Using frame", idx, "from scan", scan)
+
+        # placing the raw image
+        if fetch_raw_image:
+            raw_image = hin[scan + "/measurement/" + dset.detector][idx]
+
+    return scan, idx, raw_image