Merge pull request #385 from deepanshs/djs/review_update

Convert all MHz defaults to Hz

docs/introduction/fitting_example.rst

@@ -339,7 +339,7 @@ to be modeled with the Method class.
 
     Al27 = Isotope(symbol="27Al")
     origin_offset = spectral_dims[0]["origin_offset"]
-    B0 = Al27.ref_freq_to_B0(origin_offset / 1e6)
+    B0 = Al27.ref_freq_to_B0(origin_offset)
 
     MAS = BlochDecayCTSpectrum(
         channels=["27Al"],

docs/introduction/getting_started.rst

@@ -137,8 +137,8 @@ familiar to an NMR spectroscopist.
     from mrsimulator.spin_system.isotope import Isotope
 
     # Set the magnetic flux density in T from the proton
-    # frequency of TMS, a primary reference, in MHz
-    B0 = Isotope(symbol="1H").ref_freq_to_B0(400)
+    # frequency of TMS, a primary reference, in Hz
+    B0 = Isotope(symbol="1H").ref_freq_to_B0(400e6)
 
     # Create a BlochDecaySpectrum instance
     method = BlochDecaySpectrum(

src/mrsimulator/simulator/__init__.py

@@ -420,7 +420,7 @@ def run(
             )(jobs)
 
             B0 = method.spectral_dimensions[0].events[0].magnetic_flux_density
-            w_ref = method.channels[0].B0_to_ref_freq(B0) * 1e6
+            w_ref = method.channels[0].B0_to_ref_freq(B0)
             for seq in method.spectral_dimensions:
                 seq.origin_offset = w_ref
 

src/mrsimulator/spin_system/isotope.py

@@ -218,21 +218,21 @@ def larmor_freq(self, B0=9.4):
             float B0: magnetic field strength in T
 
         Returns:
-            float: Larmor frequency in MHz
+            float: Larmor frequency in Hz
 
         Example
         -------
 
         >>> silicon = Isotope(symbol="29Si")
         >>> freq = silicon.larmor_freq(B0 = 9.4)
         """
-        return -self.gyromagnetic_ratio * B0
+        return -self.gyromagnetic_ratio * B0 * 1.0e6
 
-    def ref_freq_to_B0(self, ref_freq=400):
+    def ref_freq_to_B0(self, ref_freq=400e6):
         """Return the magnetic field strength B0 given the primary reference frequency.
 
         Args:
-            float ref_freq: primary reference frequency in MHz
+            float ref_freq: primary reference frequency in Hz
 
         Returns:
             float: magnetic flux density in T
@@ -241,10 +241,10 @@ def ref_freq_to_B0(self, ref_freq=400):
         -------
 
         >>> H1 = Isotope(symbol="1H")
-        >>> B0 = H1.ref_freq_to_B0(ref_freq = 400)
+        >>> B0 = H1.ref_freq_to_B0(ref_freq = 400e6)
         """
         ref_ratio = self.reference.ratio / 100  # normalize reference ratio to 1
-        return 0.02348731439404777 * ref_freq / ref_ratio
+        return 1.0e-6 * 0.02348731439404777 * ref_freq / ref_ratio
 
     def B0_to_ref_freq(self, B0=9.4):
         """Return the primary reference frequency given the magnetic field strength B0.
@@ -253,7 +253,7 @@ def B0_to_ref_freq(self, B0=9.4):
             float B0: magnetic flux density in T
 
         Returns:
-            float: primary reference frequency in MHz
+            float: primary reference frequency in Hz
 
         Example
         -------
@@ -262,7 +262,7 @@ def B0_to_ref_freq(self, B0=9.4):
         >>> B0 = H1.B0_to_ref_freq(B0 = 9.4)
         """
         ref_ratio = self.reference.ratio / 100  # normalize reference ratio to 1
-        return B0 * ref_ratio / 0.02348731439404777
+        return 1.0e6 * B0 * ref_ratio / 0.02348731439404777
 
     @property
     def ref_larmor_ratio(self):

src/mrsimulator/spin_system/tests/test_isotope.py

@@ -1,3 +1,4 @@
+import numpy as np
 import pytest
 from mrsimulator.spin_system.isotope import get_isotope_dict
 from mrsimulator.spin_system.isotope import Isotope
@@ -16,9 +17,10 @@ def test_isotope():
     assert silicon.quadrupole_moment == 0.0
     assert silicon.spin == 0.5
     assert silicon.efg_to_Cq == 0
-    assert silicon.larmor_freq(B0=11.75) == 99.46962016339306
-    assert silicon.B0_to_ref_freq(B0=11.75) == 99.3895867929281
-    assert silicon.ref_freq_to_B0(ref_freq=99.3895867929281) == 11.75
+    assert np.allclose(silicon.larmor_freq(B0=11.75), 99.46962016339306e6)
+    silicon_ref_freq = 99.3895867929281e6
+    assert np.allclose(silicon.B0_to_ref_freq(B0=11.75), silicon_ref_freq)
+    assert np.allclose(silicon.ref_freq_to_B0(ref_freq=silicon_ref_freq), 11.75)
 
     proton = Isotope(symbol="1H")
     assert proton.atomic_number == 1
@@ -27,14 +29,15 @@ def test_isotope():
     assert proton.quadrupole_moment == 0.0
     assert proton.spin == 0.5
     assert silicon.efg_to_Cq == 0
-    assert proton.larmor_freq(B0=9.40) == -400.2283045725638
-    assert proton.B0_to_ref_freq(B0=9.40) == 400.21604182989006
-    assert proton.ref_freq_to_B0(ref_freq=400.21604182989006) == 9.40
+    assert np.allclose(proton.larmor_freq(B0=9.40), -400.2283045725638e6)
+    proton_ref_freq = 400.21604182989006e6
+    assert np.allclose(proton.B0_to_ref_freq(B0=9.40), proton_ref_freq)
+    assert np.allclose(proton.ref_freq_to_B0(ref_freq=proton_ref_freq), 9.40)
 
     americium = Isotope(symbol="243Am")
     assert americium.atomic_number == 95
     assert americium.reference.ratio == 10.956895712592464
-    assert americium.B0_to_ref_freq(B0=11.75) == 54.81406791045811
+    assert np.allclose(americium.B0_to_ref_freq(B0=11.75), 54.81406791045811e6)
 
     nitrogen = Isotope(symbol="14N")
     assert nitrogen.atomic_number == 7
@@ -43,9 +46,10 @@ def test_isotope():
     assert nitrogen.quadrupole_moment == 0.0193
     assert nitrogen.spin == 1
     assert nitrogen.efg_to_Cq == 4534820.208433115
-    assert nitrogen.larmor_freq(B0=18.79) == -57.830093199115574
-    assert nitrogen.B0_to_ref_freq(B0=18.79) == 57.81099284148487
-    assert nitrogen.ref_freq_to_B0(ref_freq=57.81099284148487) == 18.79
+    assert np.allclose(nitrogen.larmor_freq(B0=18.79), -57.830093199115574e6)
+    nitrogen_ref_freq = 57.81099284148487e6
+    assert np.allclose(nitrogen.B0_to_ref_freq(B0=18.79), nitrogen_ref_freq)
+    assert np.allclose(nitrogen.ref_freq_to_B0(ref_freq=nitrogen_ref_freq), 18.79)
 
     error = "Isotope symbol `x` not recognized."
     with pytest.raises(Exception, match=error):

src/mrsimulator/utils/spectral_fitting.py

@@ -614,7 +614,7 @@ def _generate_distribution_spectrum(
     """
     method = kernel.method
     isotope = method.channels[0]
-    larmor_freq = isotope.larmor_freq(B0=method.magnetic_flux_density)
+    larmor_freq = isotope.larmor_freq(B0=method.magnetic_flux_density) / 1.0e6  # MHz
     larmor_freq *= isotope.ref_larmor_ratio
     exp_spectrum = method.experiment
 

tests/2D_spectrum_tests/test_das.py

@@ -137,7 +137,7 @@ def test_DAS():
                 eta = site.quadrupolar.eta
             iso = site.isotropic_chemical_shift
             iso_obs = quad_iso_shift(
-                0.5, Cq, eta, spin, iso, larmor_freq, O17.B0_to_ref_freq(B0)
+                0.5, Cq, eta, spin, iso, larmor_freq, O17.B0_to_ref_freq(B0) / 1e6
             )
             # get the index where there is a signal
             id1 = np.real(dataset_das[i] / dataset_das[i].max())

tests/2D_spectrum_tests/test_mqmas.py

@@ -131,7 +131,7 @@ def test_ThreeQ_VAS_spin_3halves():
     # ref: D. Massiot et al. / Solid State Nuclear Magnetic Resonance 6 (1996) 73-83
     spin = method.channels[0].spin
     v0 = method.channels[0].gyromagnetic_ratio * B0 * 1e6
-    vref = method.channels[0].B0_to_ref_freq(B0) * 1e6
+    vref = method.channels[0].B0_to_ref_freq(B0)
     vq = (3 * 3.5e6) / (2 * spin * (2 * spin - 1))
     v_iso = -9 * 17 / 8 + 1e6 / 8 * (vq**2 / abs(v0 * vref)) * ((0.36**2) / 3 + 1)
 
@@ -196,7 +196,7 @@ def test_MQMAS_spin_5halves():
     # ref: D. Massiot et al. / Solid State Nuclear Magnetic Resonance 6 (1996) 73-83
     spin = method.channels[0].spin
     v0 = method.channels[0].gyromagnetic_ratio * 7 * 1e6
-    vref = method.channels[0].B0_to_ref_freq(7) * 1e6
+    vref = method.channels[0].B0_to_ref_freq(7)
     vq = 3 * 3.22e6 / (2 * spin * (2 * spin - 1))
     v_iso = -(17 / 31) * 64.5 - (8e6 / 93) * (vq**2 / abs(v0 * vref)) * (
         (0.66**2) / 3 + 1