Merge pull request #42 from gpilab/develop

Merge for version 2.3.0

.gitignore

@@ -5,4 +5,5 @@
 *.so
 *.o
 *.DS_Store
+*.zip
 build/

gridding/GPI/Grid_GPI.py

@@ -98,7 +98,7 @@ def execType(self):
     def initUI(self):
 
         # Widgets
-        self.addWidget('Slider','Dims per Set',min=1)
+        self.addWidget('Slider','Dims per Set',min=1,val=2)
         self.addWidget('SpinBox','Eff MTX XY', min=5, val=240)
         self.addWidget('SpinBox','Eff MTX Z',  min=5, val=240)
         self.addWidget('DoubleSpinBox','dx (pixels)', val=0.0)

gridding/GPI/SDC_GPI.py

@@ -67,7 +67,7 @@ def initUI(self):
 
         # Widgets
         self.addWidget('PushButton','computenow',toggle=True)
-        self.addWidget('Slider','Dims per Set',min=1)
+        self.addWidget('Slider','Dims per Set',min=1,val=2)
         self.addWidget('SpinBox','Iterations',val=1, min=1)
         self.addWidget('DoubleSpinBox','Effective MTX XY',val=300.0, min=2.0)
         self.addWidget('DoubleSpinBox','Effective MTX Z',val=300.0, min=2.0)

spiral/GPI/SpiralGenCF_GPI.py

@@ -0,0 +1,237 @@
+#     The GPI core node library is licensed under
+# either the BSD 3-clause or the LGPL v. 3.
+#
+#     Under either license, the following additional term applies:
+#
+#         NO CLINICAL USE.  THE SOFTWARE IS NOT INTENDED FOR COMMERCIAL
+# PURPOSES AND SHOULD BE USED ONLY FOR NON-COMMERCIAL RESEARCH PURPOSES.  THE
+# SOFTWARE MAY NOT IN ANY EVENT BE USED FOR ANY CLINICAL OR DIAGNOSTIC
+# PURPOSES.  YOU ACKNOWLEDGE AND AGREE THAT THE SOFTWARE IS NOT INTENDED FOR
+# USE IN ANY HIGH RISK OR STRICT LIABILITY ACTIVITY, INCLUDING BUT NOT LIMITED
+# TO LIFE SUPPORT OR EMERGENCY MEDICAL OPERATIONS OR USES.  LICENSOR MAKES NO
+# WARRANTY AND HAS NOR LIABILITY ARISING FROM ANY USE OF THE SOFTWARE IN ANY
+# HIGH RISK OR STRICT LIABILITY ACTIVITIES.
+#
+#     If you elect to license the GPI core node library under the LGPL the
+# following applies:
+#
+#         This file is part of the GPI core node library.
+#
+#         The GPI core node library is free software: you can redistribute it
+# and/or modify it under the terms of the GNU Lesser General Public License as
+# published by the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version. GPI core node library is distributed
+# in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even
+# the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Lesser General Public License for more details.
+#
+#         You should have received a copy of the GNU Lesser General Public
+# License along with the GPI core node library. If not, see
+# <http://www.gnu.org/licenses/>.
+
+
+# Author: Jim Pipe
+# Date: 2020Oct
+
+import gpi
+
+class ExternalNode(gpi.NodeAPI):
+
+    """Module to generate the gradient waveforms for a desired k-space
+    waveform. Uses the core files spiralgencf_gen.c and spiralgencf_fill.cpp
+    
+    INPUTS:
+    GIRF_in - (optional) gradient impulse response function for gradient preconditioning
+
+    OUTPUTS:
+    crds_out - output coordinates: the last dimension is 2 (kx/ky).
+    grd_out - gradient waveforms used to produce crds_out.  Dwell time is SPGRAST
+
+    WIDGETS: most widgets self-explanatory, here are a few clarifications:
+    min undersample - R, i.e. the undersampling relative to (1/FOV) before
+        kr reaches usamp st
+    max undersample - R, i.e. the undersampling relative to (1/FOV) after
+        kr exceeds usamp end
+    usamp st (0-1) - the relative value of kr at which undersampling begins (0
+        at the center, 1 at the edge of collected k-space) the samples are
+        collected at the nyquist limit (1/FOV) prior to that
+    usamp end (0-1) - the relative value of kr at which undersampling ends
+        the samples are collected at the R times the nyquist limit (1/FOV)
+        prior to that
+    Max G Freq - limits the maximum frequency of the gradient waveform during
+        the spiral readout. If set to 0, there is no limit (default minimum is 0.5 kHz)
+    Start Window - time for rounding enforced when starting
+    Corner Window - an angle determining the rounding enforced when
+        transitioning between (freq, slew,grad) limits
+    spinout - controls spiral in, out, etc.
+        OUT - generate spiral-out waveform
+        IN  - generate spiral-in waveform
+        OUT180 - generate spiral-out waveform and negate the waveform
+
+    ****************************************
+    *** The concept of "true resolution" ***
+    k-space data are typically normalized, for the gridding process, to values
+    between -0.5 and 0.5 For spiral data (which measure circular k-space) to
+    have the same resolution as Cartesian (square k-space) they must measure a
+    diameter of 2/sqrt(pi) ~ 1.13 larger than conventional k-space limits (so
+    that the area of the circle equals the area of the square).  k-space
+    coordinates, therefore, are multiplied by 0.8, so that their range of
+    0.8*2/sqrt(pi) = 0.903, or -0.451 to +0.451, fits within the gridded space.
+    The resulting image, with no further zero-padding, will have pixels that
+    are 0.8 times smaller than the requested resolution, with a matrix 25%
+    larger in each dimension.  This is a semi-complicated way of making sure
+    that this works routinely, and is referred to by the authors as "true
+    resolution".
+    *****************************************
+    """
+
+    def execType(self):
+        return gpi.GPI_PROCESS
+
+    def initUI(self):
+
+        import numpy as np
+
+        # Widgets
+        self.addWidget('PushButton', 'compute', toggle=True)
+        self.addWidget('TextBox', 'Info:')
+
+        self.addWidget('DoubleSpinBox', 'FOV (cm)',
+                       val=24.0, min=0.1, decimals=6)
+        self.addWidget('DoubleSpinBox', 'Res (mm)',
+                       val=0.8, min=0.1, singlestep=0.1, decimals=5)
+        self.addWidget('SpinBox', '# of Spiral Arms', val=16, min=1)
+
+        self.addWidget('ExclusivePushButtons', 'spinout',
+                       buttons=['OUT', 'IN', 'OUT180'],val=0)
+
+        self.addWidget('DoubleSpinBox', 'AD dwell time (us)',
+                       val=1.0, min=0.1, decimals=6)
+        self.addWidget('DoubleSpinBox', 'MaxSlw (mT/m/ms)',
+                       val=150.0, min=0.01, decimals=6)
+        self.addWidget('DoubleSpinBox', 'MaxGrd (mT/m)',
+                       val=40.0, min=0.01, decimals=6)
+
+        self.addWidget('DoubleSpinBox', 'min undersample',
+                       val=1.0, min=0.0, max=100.0)
+        self.addWidget('DoubleSpinBox', 'max undersample',
+                       val=1.0, min=0.0, max=100.0)
+        self.addWidget('DoubleSpinBox', 'usamp st (0 - 1)',
+                       val=0.0, min=0.0, max=1.0, singlestep=0.01)
+        self.addWidget('DoubleSpinBox', 'usamp end (0 - 1)',
+                       val=1.0, min=0.0, max=1.0, singlestep=0.01)
+
+        self.addWidget('PushButton', 'Precompensate', toggle=True, val=1)
+        self.addWidget('PushButton', 'Precondition', toggle=True, val=1)
+
+        self.addWidget('DoubleSpinBox', 'Max G Freq (kHz)', val=1.0, min=0.5, max=20.)
+        self.addWidget('DoubleSpinBox', 'Start Window (us)', val=200.0, min=0.0)
+        self.addWidget('DoubleSpinBox', 'End Window (us)', val=100.0, min=0.0)
+        self.addWidget('DoubleSpinBox', 'Corner Window (cycles)', val=0.5, min=0.0)
+
+        self.addWidget('DoubleSpinBox', 'TrueRes Factor', val=1.0,
+                       min=0.0, max=1.0)
+
+        self.addWidget('DoubleSpinBox', 'x delay (us)',
+                       val=0.0, min=-100.0, max=100.0, visible = False)
+        self.addWidget('DoubleSpinBox', 'y delay (us)',
+                       val=0.0, min=-100.0, max=100.0, visible = False)
+
+        self.addWidget('DoubleSpinBox', 'Gam (kHz/mT)',
+                       val=42.577, min=0.01, decimals=6, visible = False) # hide this until we need it
+
+        # IO Ports
+        self.addInPort('GIRF_in', 'NPYarray',dtype=[np.float32,np.float64],ndim=1,obligation=gpi.OPTIONAL)
+        self.addOutPort('crds_out', 'NPYarray')
+        self.addOutPort('grd_out', 'NPYarray')
+        self.addOutPort('gtf_out', 'NPYarray')
+
+    def compute(self):
+
+        import numpy as np
+
+        # convert units to ms, kHz, m, mT
+        dwell = 0.001 * self.getVal('AD dwell time (us)')
+        xdely = 0.001 * self.getVal('x delay (us)')
+        ydely = 0.001 * self.getVal('y delay (us)')
+
+        mslew = self.getVal('MaxSlw (mT/m/ms)')
+        mgrad = self.getVal('MaxGrd (mT/m)')
+        gamma = self.getVal('Gam (kHz/mT)')
+
+        fov = 0.01 * self.getVal('FOV (cm)')
+
+        narms = float(self.getVal('# of Spiral Arms'))
+
+        trures_fac = self.getVal('TrueRes Factor')
+        trures_acq = trures_fac * np.sqrt(np.pi)/2 + 1 - trures_fac
+
+        res = 0.001 * self.getVal('Res (mm)')
+
+        us_0 = self.getVal('usamp st (0 - 1)')
+        us_1 = self.getVal('usamp end (0 - 1)')
+        us_r0 = self.getVal('min undersample')
+        us_r = self.getVal('max undersample')
+
+        precomp = self.getVal('Precompensate')
+        precond = self.getVal('Precondition')
+
+        mgfrq = self.getVal('Max G Freq (kHz)')
+        start_win = 0.001*self.getVal('Start Window (us)') # change to ms
+        end_win = 0.001*self.getVal('End Window (us)') # change to ms
+        corner_win = 2.*np.pi*self.getVal('Corner Window (cycles)') # change to radians
+
+        spinout = self.getVal('spinout')
+
+        if self.getVal('compute'):
+
+            girf = self.getData('GIRF_in')
+            if girf is not None:
+              # The first point should not be 0
+              while girf[0] == 0:
+                girf = girf[1:]
+              # normalize to have unit area, so DC part of MTF is 1
+              girf = np.float64(girf)/np.sum(np.float64(girf))
+            else:
+              # Make it a delta function
+              girf = np.float64(np.array([1.,0.]))
+
+            gtf_res = 0.05 # spectral resolution in kHz
+            spgrast = 0.005 # gradient raster in ms
+            # gtf_len*spgrast = 1/gtf_res
+            # force gtf_len to be even
+            gtf_len = 2*int(0.5/(gtf_res*spgrast))
+
+            gtf = np.absolute(np.fft.fft(np.pad(girf,(0,gtf_len-girf.shape[0]))))
+
+            # import in thread to save namespace
+            # spiralgencf corresponds to spiralgencf_PyMOD.cpp
+            import gpi_core.spiral.spiralgencf as sp
+
+            print("end win",end_win)
+            grd_out, crds_out = sp.coords(
+                girf,gtf,dwell, xdely, ydely, mslew, mgrad, gamma,
+                fov, res, narms,
+                us_0, us_1, us_r0, us_r,
+                mgfrq, precomp, precond, start_win, end_win, corner_win, spinout,
+                trures_acq)
+
+            # Report Back to User
+            nsamp = np.array(crds_out.shape)[-2]
+
+            spgrast = 0.005 # Gradient raster time in ms
+
+            smp = "Samples: " + str(nsamp) + "\n"
+            tau = "Tau (ms): " + str(dwell * nsamp) + "\n"
+            tgrad = spgrast * np.array(grd_out.shape)[1]
+            tgr = "TGrad (ms): " + str(tgrad) + "\n"
+            info = smp + tau + tgr
+            self.setAttr('Info:', val=info)
+
+            grd_out = grd_out[..., 0:2]
+
+            self.setData('crds_out', crds_out)
+            self.setData('grd_out', grd_out)
+            self.setData('gtf_out', gtf)
+
+        return(0)