Merge pull request #261 from CJ-Wright/tomo_3D

Support 3D pencil reconstruction

docs/_templates/using_servers.rst

@@ -46,10 +46,11 @@ folders.
 Users will need to specify which folder(s) they would like the data to be
 placed in before running their experiments.',
 qoi='The QOI server performs additional data processing and analysis,
-extracting quantities of interest from raw and reduced data.
+extracting quantities of interest from raw and reduced data.',
 viz='The viz server visualizes raw and processed data as it becomes available.
 This server should already be running, only beamline staff should need to
-start it.'
+start it.',
+tomo='The tomo server runs tomographic reconstructions on all scalar data (raw and analyzed). The reconstruction algorithm can be changed via the ``algorithm`` keyword.'
 ) %}
 
 {% for name, blurb in servers_dict.items() %}

examples/ctPDF_example.py

@@ -0,0 +1,49 @@
+import os
+import time
+
+import bluesky.plans as bp
+import dxchange
+import numpy as np
+import tomopy
+from bluesky.run_engine import RunEngine
+from ophyd.sim import SynSignal, hw
+from xpdan.vend.callbacks.zmq import Publisher
+from xpdconf.conf import glbl_dict
+
+hw = hw()
+rot_center = 290
+m = hw.motor1
+m.kind = "hinted"
+mm = hw.motor2
+mm.kind = "hinted"
+mmm = hw.motor3
+mmm.kind = "hinted"
+xrun(0,
+    bp.grid_scan(
+        [xpd_pe1c],
+        mmm,
+        0,
+        2,
+        2,
+        m,
+        0,
+        180,
+        4,
+        True,
+        mm,
+        200,
+        401,
+        4,
+        True,
+
+        md={
+            "tomo": {
+                "type": "pencil",
+                "rotation": "motor1",
+                "translation": "motor2",
+                "stack": "motor3",
+                "center": rot_center - 200,
+            }
+        },
+    )
+)

examples/multi_tomo_example.py

@@ -0,0 +1,151 @@
+import os
+import time
+
+import bluesky.plans as bp
+import dxchange
+import numpy as np
+import tomopy
+from bluesky.run_engine import RunEngine
+from ophyd.sim import SynSignal, hw, SynSignalWithRegistry
+from xpdan.vend.callbacks.zmq import Publisher
+from xpdconf.conf import glbl_dict
+
+hw = hw()
+fname = os.path.expanduser("~/Downloads/tooth.h5")
+
+proj, flat, dark, theta = dxchange.read_aps_32id(fname, sino=(0, 1))
+
+proj = tomopy.normalize(proj, flat, dark)
+
+rot_center = tomopy.find_center(proj, theta, init=290, ind=0, tol=0.5)
+# proj2 = np.hstack((proj[:, :, :],) * 200)
+# proj2 = np.hstack((proj[:, :, :],) * 1)
+# rot_center -= 200
+proj2 = proj
+m = hw.motor1
+m.kind = "hinted"
+mm = hw.motor2
+mm.kind = "hinted"
+mmm = hw.motor3
+mmm.kind = "hinted"
+
+
+class FullField:
+    def __call__(self, *args, **kwargs):
+        v = m.get()[0]
+        out = proj2[int(v), :, :]
+        print(v)
+        time.sleep(.5)
+        return out
+
+
+class Pencil:
+    def __call__(self, *args, **kwargs):
+        v = m.get()[0]
+        vv = mm.get()[0]
+        out = proj2[int(v), :, int(vv)]
+        print(v, vv, mmm.get()[0])
+        time.sleep(.5)
+        return np.squeeze(out)
+
+
+f = FullField()
+# det = SynSignal(f, name="img", labels={"detectors"})
+det = SynSignalWithRegistry(f, name="img", labels={"detectors"},)
+det.kind = "hinted"
+
+#g = Pencil()
+#det2 = SynSignal(g, name="img", labels={"detectors"})
+#det2.kind = "hinted"
+
+RE = RunEngine()
+RE.md['analysis_stage'] = 'raw'
+p = Publisher(glbl_dict["inbound_proxy_address"], prefix=b"raw")
+t = RE.subscribe(p)
+# RE.subscribe(print)
+
+# Build scan
+l = [0, 90]
+for i in range(8):
+    ll = l.copy()
+    interval = sorted(set(ll))[1] / 2
+    for lll in ll:
+        j = lll + interval
+        j = round(j, 0)
+        if j not in l and j < 180:
+            l.append(j)
+# Run Full Field Scans, each scan has more slices, showing how we can minimize
+# the number of slices by interleaving them by half
+for i in [2 ** n for n in range(2, 8)] + [180]:
+    RE(
+        bp.list_scan(
+            [det],
+            m,
+            l[:i],
+            md={
+                "tomo": {
+                    "type": "full_field",
+                    "rotation": "motor1",
+                    "center": rot_center,
+                }
+            },
+        )
+    )
+    print(i)
+    time.sleep(3)
+'''
+# Run in pencil beam geometry (this takes a long time!)
+RE(
+    bp.grid_scan(
+        [det2],
+        m,
+        0,
+        180,
+        181,
+        mm,
+        0,
+        639,
+        640,
+        True,
+        md={
+            "tomo": {
+                "type": "pencil",
+                "rotation": "motor1",
+                "translation": "motor2",
+                "center": rot_center,
+            }
+        },
+    )
+)
+# Run in 3D pencil beam geometry
+RE(
+    bp.grid_scan(
+        [det2],
+        mmm,
+        0,
+        2,
+        10,
+        m,
+        0,
+        180,
+        41,
+        True,
+        mm,
+        200,
+        401,
+        21,
+        True,
+
+        md={
+            "tomo": {
+                "type": "pencil",
+                "rotation": "motor1",
+                "translation": "motor2",
+                "stack": "motor3",
+                "center": rot_center - 200,
+            }
+        },
+    )
+)
+RE.abort()
+'''

examples/tomo_example.py

@@ -6,7 +6,7 @@
 import numpy as np
 import tomopy
 from bluesky.run_engine import RunEngine
-from ophyd.sim import SynSignal, hw
+from ophyd.sim import SynSignal, hw, SynSignalWithRegistry
 from xpdan.vend.callbacks.zmq import Publisher
 from xpdconf.conf import glbl_dict
 
@@ -26,6 +26,8 @@
 m.kind = "hinted"
 mm = hw.motor2
 mm.kind = "hinted"
+mmm = hw.motor3
+mmm.kind = "hinted"
 
 
 class FullField:
@@ -42,23 +44,26 @@ def __call__(self, *args, **kwargs):
         v = m.get()[0]
         vv = mm.get()[0]
         out = proj2[int(v), :, int(vv)]
-        print(v, vv)
-        time.sleep(.1)
+        print(v, vv, mmm.get()[0])
+        time.sleep(.5)
         return np.squeeze(out)
 
 
 f = FullField()
-det = SynSignal(f, name="img", labels={"detectors"})
+# det = SynSignal(f, name="img", labels={"detectors"})
+det = SynSignalWithRegistry(f, name="img", labels={"detectors"},)
 det.kind = "hinted"
 
-g = Pencil()
-det2 = SynSignal(g, name="img", labels={"detectors"})
-det2.kind = "hinted"
+#g = Pencil()
+#det2 = SynSignal(g, name="img", labels={"detectors"})
+#det2.kind = "hinted"
 
 RE = RunEngine()
+RE.md['analysis_stage'] = 'raw'
 p = Publisher(glbl_dict["inbound_proxy_address"], prefix=b"raw")
 t = RE.subscribe(p)
 # RE.subscribe(print)
+
 # Build scan
 l = [0, 90]
 for i in range(8):
@@ -71,7 +76,7 @@ def __call__(self, *args, **kwargs):
             l.append(j)
 # Run Full Field Scans, each scan has more slices, showing how we can minimize
 # the number of slices by interleaving them by half
-for i in [2 ** n for n in range(2, 8)] + [180]:
+for i in [180]:
     RE(
         bp.list_scan(
             [det],
@@ -88,6 +93,7 @@ def __call__(self, *args, **kwargs):
     )
     print(i)
     time.sleep(3)
+'''
 # Run in pencil beam geometry (this takes a long time!)
 RE(
     bp.grid_scan(
@@ -111,4 +117,35 @@ def __call__(self, *args, **kwargs):
         },
     )
 )
+# Run in 3D pencil beam geometry
+RE(
+    bp.grid_scan(
+        [det2],
+        mmm,
+        0,
+        2,
+        10,
+        m,
+        0,
+        180,
+        41,
+        True,
+        mm,
+        200,
+        401,
+        21,
+        True,
+
+        md={
+            "tomo": {
+                "type": "pencil",
+                "rotation": "motor1",
+                "translation": "motor2",
+                "stack": "motor3",
+                "center": rot_center - 200,
+            }
+        },
+    )
+)
 RE.abort()
+'''

news/tomo_3D

@@ -0,0 +1,19 @@
+**Added:**
+
+* Support for 3D pencil beam reconstructions
+* Support for Registry backed full field reconstructions
+* ``ctPDF_example.py`` example for pencil beam
+
+**Changed:**
+
+* ``tomo_example.py`` runs on a registry backed detector
+
+**Deprecated:** None
+
+**Removed:** None
+
+**Fixed:**
+
+* Pencil beam no longer tries to run independent var reconstructions
+
+**Security:** None

setup.py

@@ -7,6 +7,7 @@
     "viz_server",
     "analysis_server",
     "qoi_server",
+    "tomo_server",
 ]
 
 entry_points = {