Refs #53. first try

python/imars3d/CT.py

@@ -68,17 +68,19 @@ def recon(self, workdir=None, outdir=None, **kwds):
         if self.clean_on_the_fly:
             cropped.removeAll()
         # correct tilt
-        for i in range(3):
+        MAX_TILT_ALLOWED = 0.05
+        NROUNDS = 3
+        for i in range(NROUNDS):
             tilt_corrected, tilt = i3.correct_tilt(
                 pre, workdir=os.path.join(workdir, 'tilt-correction-%s' % i),
                 max_npairs=None, parallel=self.parallel_preprocessing)
             if self.clean_on_the_fly:
                 pre.removeAll()
-            if abs(tilt) < .5: break
+            if abs(tilt) < MAX_TILT_ALLOWED: break
             pre = tilt_corrected
             continue
-        if abs(tilt) >= .5:
-            raise RuntimeError("failed to bring tilt down to less than .5 degrees in 3 rounds")
+        if abs(tilt) >= MAX_TILT_ALLOWED:
+            raise RuntimeError("failed to bring tilt down to less than %s degrees in %s rounds" % (MAX_TILT_ALLOWED, NROUNDS))
         # reconstruct
         self.reconstruct(tilt_corrected, workdir=workdir, outdir=outdir, **kwds)
         return
@@ -217,7 +219,7 @@ def sniff(self):
         return
 
     CT_pattern_cache = "CT_PATTERN"
-    CT_angles_cache = "CT_ANGLES"
+    CT_angles_cache = "CT_ANGLES.npy"
     def find_CT(self):
         pattern_cache_path = os.path.join(self.workdir, self.CT_pattern_cache)
         angles_cache_path = os.path.join(self.workdir, self.CT_angles_cache)

python/imars3d/__init__.py

@@ -72,14 +72,18 @@ def correct_tilt(ct_series, workdir='work', max_npairs=10, parallel=True):
     tiltcalc = components.TiltCalculation(workdir=workdir, max_npairs=max_npairs)
     tilt = tiltcalc(ct_series)
 
-    tiltcorrected_series = io.ImageFileSeries(
-        os.path.join(workdir, "tiltcorrected_%07.3f.tiff"),
-        identifiers = ct_series.identifiers,
-        name = "Tilt corrected CT", mode = 'w',
-    )
-    tiltcorr = components.TiltCorrection(tilt=tilt)
-    tiltcorr(ct_series, tiltcorrected_series, parallel=parallel)
-    return tiltcorrected_series, tilt
+    # only correct if the tilt is large
+    if abs(tilt)>0.002:
+        tiltcorrected_series = io.ImageFileSeries(
+            os.path.join(workdir, "tiltcorrected_%07.3f.tiff"),
+            identifiers = ct_series.identifiers,
+            name = "Tilt corrected CT", mode = 'w',
+        )
+        tiltcorr = components.TiltCorrection(tilt=tilt)
+        tiltcorr(ct_series, tiltcorrected_series, parallel=parallel)
+        return tiltcorrected_series, tilt
+    return ct_series, tilt
+
 
 @dec.timeit
 def correct_intensity_fluctuation(ct_series, workdir='work'):

python/imars3d/tilt/__init__.py

@@ -2,8 +2,22 @@
 
 import os, numpy as np
 import logging
+from . import use_centers, phasecorrelation
 
-def compute(ct_series, workdir, max_npairs=10, calculator=None):
+def compute(ct_series, workdir, max_npairs=10):
+    from . import use_centers
+    calculator = use_centers.Calculator(sigma=10, maxshift=200)
+    tilt = _compute(
+        ct_series, os.path.join(workdir, 'testrun'), max_npairs=10,
+        calculator=calculator)
+    if abs(tilt) > 0.8:
+        calculator = phasecorrelation.PhaseCorrelation()
+        tilt = _compute(
+            ct_series, workdir, max_npairs=max_npairs,
+            calculator=calculator)
+    return tilt
+
+def _compute(ct_series, workdir, max_npairs=10, calculator=None):
     logger = logging.getLogger("imars3d.tilt")
     tilt_out = os.path.join(workdir, "tilt.out")
     # cached value?
@@ -13,7 +27,6 @@ def compute(ct_series, workdir, max_npairs=10, calculator=None):
     if not calculator:
         # from . import phasecorrelation
         # calculator = phasecorrelation.PhaseCorrelation()
-        from . import use_centers
         calculator = use_centers.Calculator(sigma=10, maxshift=200)
     img = lambda angle: ct_series.getImage(angle)
     # find opposite pairs
@@ -67,11 +80,13 @@ def check(tilt, img0, img180):
 def apply(tilt, img, outimg, save=True):
     """apply tilt to the given image
     """
-    from scipy import ndimage
+    # from scipy import ndimage
+    from skimage.transform import rotate
     import numpy as np
 
     data = img.getData()
-    data = ndimage.rotate(data, -tilt)
+    # data = ndimage.rotate(data, -tilt)
+    data = rotate(data, -tilt)
     outimg.data = data
     if save:
         outimg.save()

python/imars3d/tilt/use_centers.py

@@ -14,7 +14,7 @@ def __init__(self, logging_dir=None, **opts):
     def __call__(self, img0, img180):
         slope, intercept = computeTilt(img0, img180, workdir=self.logging_dir, **self.opts)
         # print (slope, np.arctan(slope))
-        return np.arctan(slope)*180./np.pi, 1.0
+        return .7 * np.arctan(slope)*180./np.pi, 1.0
 
 
 def computeTilt(img0, img180, workdir=None, **kwds):