Merge branch 'master' into djs/docs

.github/workflows/continuous-integration-pip.yml

@@ -69,7 +69,9 @@ jobs:
         run: python setup.py develop
 
       - name: Test with pytest
-        run: pytest --cov=./ --cov-report=xml
+        run: |
+          python -m pip install pytest -U
+          pytest --cov=./ --cov-report=xml
 
       - name: Upload coverage
         uses: codecov/[email protected]
@@ -103,7 +105,9 @@ jobs:
         run: python setup.py develop
 
       - name: Test with pytest
-        run: pytest --cov=./ --cov-report=xml
+        run: |
+          python -m pip install pytest -U
+          pytest --cov=./ --cov-report=xml
 
       - name: Upload coverage
         uses: codecov/[email protected]
@@ -137,7 +141,9 @@ jobs:
         run: python setup.py develop
 
       - name: Test with pytest
-        run: pytest --cov=./ --cov-report=xml
+        run: |
+          python -m pip install pytest -U
+          pytest --cov=./ --cov-report=xml
 
       - name: Upload coverage
         uses: codecov/[email protected]
@@ -152,6 +158,7 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+
       - name: Setup Miniconda
         uses: conda-incubator/setup-miniconda@v3
         env:
@@ -166,14 +173,19 @@ jobs:
       - run: |
           conda --version
           which python
+
       - name: Build and install package from source
         shell: pwsh
         run: |
           conda --version
           which python
           python setup.py develop
+
       - name: Test with pytest
         shell: pwsh
-        run: pytest --cov=./ --cov-report=xml
+        run: |
+          python -m pip install pytest -U
+          pytest --cov=./ --cov-report=xml
+
       - name: Upload coverage
         uses: codecov/[email protected]

src/c_lib/base/base_model.pxd

@@ -36,7 +36,8 @@ cdef extern from "schemes.h":
                             bool_t allow_4th_rank,
                             unsigned int n_gamma,
                             unsigned int integration_volume,
-                            bool_t interpolation)
+                            bool_t interpolation,
+                            bool_t is_complex)
 
     MRS_averaging_scheme *MRS_create_averaging_scheme_from_alpha_beta(
                             double *alpha,
@@ -47,7 +48,8 @@ cdef extern from "schemes.h":
                             unsigned int n_gamma,
                             unsigned int position_size,
                             int32_t *positions,
-                            bool_t interpolation)
+                            bool_t interpolation,
+                            bool_t is_complex)
 
     void MRS_free_averaging_scheme(MRS_averaging_scheme *scheme)
     MRS_fftw_scheme *create_fftw_scheme(unsigned int total_orientations,

src/c_lib/base/base_model.pyx

@@ -25,6 +25,7 @@ def core_simulator(method,
        unsigned int integration_volume=1,
        unsigned int isotropic_interpolation=0,
        unsigned int number_of_gamma_angles=1,
+       bool_t is_complex=True,
        bool_t interpolation=True,
        bool_t auto_switch=True,
        debug=False,
@@ -66,13 +67,14 @@ def core_simulator(method,
         averaging_scheme = clib.MRS_create_averaging_scheme_from_alpha_beta(
             alpha=&alpha[0], beta=&beta[0], weight=&weight[0], n_angles=alpha.size,
             allow_4th_rank=allow_4th_rank, n_gamma=number_of_gamma_angles,
-            position_size=position_size, positions=&positions[0], interpolation=interpolation
+            position_size=position_size, positions=&positions[0], interpolation=interpolation,
+            is_complex=is_complex
         )
     else:
         averaging_scheme = clib.MRS_create_averaging_scheme(
             integration_density=integration_density, allow_4th_rank=allow_4th_rank,
             n_gamma=number_of_gamma_angles, integration_volume=integration_volume,
-            interpolation=interpolation
+            interpolation=interpolation, is_complex=is_complex
         )
 
 # create C spectral dimensions ________________________________________________

src/c_lib/include/interpolation.h

@@ -32,7 +32,7 @@ extern void one_d_averaging(double *spec, const unsigned int freq_size, double *
                             double *amp_real, double *amp_imag, int dimension_count,
                             const unsigned int position_size, int32_t *positions,
                             const unsigned int nt, bool user_defined,
-                            bool interpolation);
+                            bool interpolation, bool is_complex);
 
 extern void two_d_averaging(double *spec, const unsigned int freq_size, double *freq1,
                             double *freq2, double *amp, int amp_stride,

src/c_lib/include/schemes.h

@@ -60,6 +60,7 @@ typedef struct MRS_averaging_scheme {
   unsigned int position_size;  // number of triangle vertexes (faces) on mesh
   bool user_defined;           // if true, the scheme is user defined
   bool interpolation;          // if true, use frequency triangle interpolation
+  bool is_complex;             // return cmoplex simulation
 } MRS_averaging_scheme;
 
 // typedef struct MRS_averaging_scheme;
@@ -86,7 +87,7 @@ MRS_averaging_scheme *MRS_create_averaging_scheme(unsigned int integration_densi
                                                   bool allow_4th_rank,
                                                   unsigned int n_gamma,
                                                   unsigned int integration_volume,
-                                                  bool interpolation);
+                                                  bool interpolation, bool is_complex);
 
 /**
  * Create a new orientation averaging scheme from given alpha and beta.
@@ -109,7 +110,7 @@ MRS_averaging_scheme *MRS_create_averaging_scheme(unsigned int integration_densi
 MRS_averaging_scheme *MRS_create_averaging_scheme_from_alpha_beta(
     double *alpha, double *beta, double *weight, unsigned int n_angles,
     bool allow_4th_rank, unsigned int n_gamma, const unsigned int position_size,
-    int32_t *positions, bool interpolation);
+    int32_t *positions, bool interpolation, bool is_complex);
 
 /**
  * Free the memory allocated for the spatial orientation averaging scheme.

src/c_lib/lib/frequency_averaging.c

@@ -117,13 +117,17 @@ void one_dimensional_averaging(MRS_dimension *dimensions, MRS_averaging_scheme *
           // multiply phase to the amplitudes.
           vm_double_multiply(scheme->total_orientations, phase_ptr, 2, &amps[k1],
                              amps_real);
-          vm_double_multiply(scheme->total_orientations, phase_ptr + 1, 2, &amps[k1],
-                             amps_imag);
+          if (scheme->is_complex) {
+            vm_double_multiply(scheme->total_orientations, phase_ptr + 1, 2, &amps[k1],
+                               amps_imag);
+          }
           while (j++ < planA->n_octants) {
             octahedronDeltaInterpolation(nt, &offset, &amps_real[address], 1,
                                          dimensions->count, spec, iso_intrp);
-            octahedronDeltaInterpolation(nt, &offset, &amps_imag[address], 1,
-                                         dimensions->count, spec + 1, iso_intrp);
+            if (scheme->is_complex) {
+              octahedronDeltaInterpolation(nt, &offset, &amps_imag[address], 1,
+                                           dimensions->count, spec + 1, iso_intrp);
+            }
             address += npts;
           }
         }
@@ -139,16 +143,18 @@ void one_dimensional_averaging(MRS_dimension *dimensions, MRS_averaging_scheme *
           // multiply phase to the amplitudes.
           vm_double_multiply(scheme->total_orientations, phase_ptr, 2, &amps[k1],
                              amps_real);
-          vm_double_multiply(scheme->total_orientations, phase_ptr + 1, 2, &amps[k1],
-                             amps_imag);
+          if (scheme->is_complex) {
+            vm_double_multiply(scheme->total_orientations, phase_ptr + 1, 2, &amps[k1],
+                               amps_imag);
+          }
           for (j = 0; j < planA->n_octants; j++) {
             // Add offset(isotropic + sideband_order) to the local frequencies.
             vm_double_add_offset(npts, &freq[address], offset, dimensions->freq_offset);
             // Perform tenting on every sideband order over all orientations.
             one_d_averaging(spec, npts, dimensions->freq_offset, &amps_real[address],
                             &amps_imag[address], dimensions->count,
                             scheme->position_size, scheme->positions, nt, user_defined,
-                            interpolation);
+                            interpolation, scheme->is_complex);
             address += npts;
           }
         }
@@ -270,12 +276,15 @@ void two_dimensional_averaging(MRS_dimension *dimensions, MRS_averaging_scheme *
                               dimensions[0].count, dimensions[1].count, iso_intrp,
                               scheme->integration_density, user_defined, interpolation);
 
-              // imaginary part
-              two_d_averaging(spec + 1, npts, dimensions[0].freq_offset,
-                              dimensions[1].freq_offset, freq_amp + 1, 2,
-                              scheme->position_size, scheme->positions,
-                              dimensions[0].count, dimensions[1].count, iso_intrp,
-                              scheme->integration_density, user_defined, interpolation);
+              if (scheme->is_complex) {
+                // imaginary part
+                two_d_averaging(spec + 1, npts, dimensions[0].freq_offset,
+                                dimensions[1].freq_offset, freq_amp + 1, 2,
+                                scheme->position_size, scheme->positions,
+                                dimensions[0].count, dimensions[1].count, iso_intrp,
+                                scheme->integration_density, user_defined,
+                                interpolation);
+              }
             }
           }
         }

src/c_lib/lib/interpolation.c

@@ -912,20 +912,27 @@ void hist1d(double *spec, const unsigned int freq_size, double *freq, double *am
 void one_d_averaging(double *spec, const unsigned int freq_size, double *freq,
                      double *amp_real, double *amp_imag, int dimension_count,
                      const unsigned int position_size, int32_t *positions,
-                     const unsigned int nt, bool user_defined, bool interpolation) {
+                     const unsigned int nt, bool user_defined, bool interpolation,
+                     bool is_complex) {
   if (!user_defined) {
     if (interpolation) {
       octahedronInterpolation(spec, freq, nt, amp_real, 1, dimension_count);
-      octahedronInterpolation(spec + 1, freq, nt, amp_imag, 1, dimension_count);
+      if (is_complex) {
+        octahedronInterpolation(spec + 1, freq, nt, amp_imag, 1, dimension_count);
+      }
     } else {
       hist1d(spec, freq_size, freq, amp_real, dimension_count, nt);
-      hist1d(spec + 1, freq_size, freq, amp_imag, dimension_count, nt);
+      if (is_complex) {
+        hist1d(spec + 1, freq_size, freq, amp_imag, dimension_count, nt);
+      }
     }
   } else {
     generic_1d_triangle_average(spec, freq_size, freq, amp_real, dimension_count,
                                 position_size, positions, nt);
-    generic_1d_triangle_average(spec + 1, freq_size, freq, amp_imag, dimension_count,
-                                position_size, positions, nt);
+    if (is_complex) {
+      generic_1d_triangle_average(spec + 1, freq_size, freq, amp_imag, dimension_count,
+                                  position_size, positions, nt);
+    }
   }
 }
 

src/c_lib/lib/schemes.c

@@ -139,7 +139,7 @@ MRS_averaging_scheme *MRS_create_averaging_scheme(unsigned int integration_densi
                                                   bool allow_4th_rank,
                                                   unsigned int n_gamma,
                                                   unsigned int integration_volume,
-                                                  bool interpolation) {
+                                                  bool interpolation, bool is_complex) {
   int alpha_size;
   MRS_averaging_scheme *scheme = malloc(sizeof(MRS_averaging_scheme));
 
@@ -151,6 +151,7 @@ MRS_averaging_scheme *MRS_create_averaging_scheme(unsigned int integration_densi
   scheme->integration_density = integration_density;
   scheme->integration_volume = integration_volume;
   scheme->allow_4th_rank = allow_4th_rank;
+  scheme->is_complex = is_complex;
 
   scheme->octant_orientations =
       ((integration_density + 1) * (integration_density + 2)) / 2;
@@ -196,7 +197,7 @@ MRS_averaging_scheme *MRS_create_averaging_scheme(unsigned int integration_densi
 MRS_averaging_scheme *MRS_create_averaging_scheme_from_alpha_beta(
     double *alpha, double *beta, double *weight, unsigned int n_angles,
     bool allow_4th_rank, unsigned int n_gamma, const unsigned int position_size,
-    int32_t *positions, bool interpolation) {
+    int32_t *positions, bool interpolation, bool is_complex) {
   double scale;
   MRS_averaging_scheme *scheme = malloc(sizeof(MRS_averaging_scheme));
 
@@ -208,6 +209,7 @@ MRS_averaging_scheme *MRS_create_averaging_scheme_from_alpha_beta(
   scheme->integration_density = 0;
   scheme->integration_volume = 0;
   scheme->allow_4th_rank = allow_4th_rank;
+  scheme->is_complex = is_complex;
 
   scheme->octant_orientations = n_angles;
 

src/c_lib/lib/simulation.c

@@ -187,6 +187,7 @@ void mrsimulator_core(
 
   bool allow_4th_rank = false;
   bool interpolation = true;
+  bool is_complex = true;
 
   if (sites[0].spin[0] > 0.5 && quad_second_order == 1) {
     allow_4th_rank = true;
@@ -199,8 +200,9 @@ void mrsimulator_core(
     number_of_sidebands = 1;
   }
 
-  MRS_averaging_scheme *scheme = MRS_create_averaging_scheme(
-      integration_density, allow_4th_rank, 9, integration_volume, interpolation);
+  MRS_averaging_scheme *scheme =
+      MRS_create_averaging_scheme(integration_density, allow_4th_rank, 9,
+                                  integration_volume, interpolation, is_complex);
 
   MRS_fftw_scheme *fftw_scheme =
       create_fftw_scheme(scheme->total_orientations, number_of_sidebands);

src/c_lib/sandbox/sandbox.pxd

@@ -21,15 +21,17 @@ cdef extern from "schemes.h":
                             bool_t allow_4th_rank,
                             unsigned int n_gamma,
                             unsigned int integration_volume,
-                            bool_t interpolation)
+                            bool_t interpolation,
+                            bool_t is_complex)
 
     MRS_averaging_scheme *MRS_create_averaging_scheme_from_alpha_beta(
                             double *alpha, double *beta,
                             double *weight, unsigned int n_angles,
                             bool_t allow_4th_rank,
                             const unsigned int position_size,
                             int32_t *positions,
-                            bool_t interpolation)
+                            bool_t interpolation,
+                            bool_t is_complex)
 
     void MRS_free_averaging_scheme(MRS_averaging_scheme *scheme)
 

src/c_lib/sandbox/sandbox.pyx

@@ -78,11 +78,12 @@ cdef class AveragingScheme:
             allow_4th_rank: Boolean, If True, pre-calculates tables for computing fourth rank tensors.
         """
         self.allow_4th_rank = allow_4th_rank
+        is_complex = True
         integration_volume_ = 0
         if integration_volume == 'hemisphere':
             integration_volume_=1
         self.scheme = clib.MRS_create_averaging_scheme(integration_density,
-                                    allow_4th_rank, 9, integration_volume_)
+                                    allow_4th_rank, 9, integration_volume_, is_complex)
 
     @property
     def interpolation(self):

src/mrsimulator/simulator/config.py

@@ -128,6 +128,10 @@ class ConfigSimulator(Parseable):
         A CustomSampling object specifying the coordinates and weights used in powder
         averaging.
 
+    is_complex: bool
+        When True, the simulation computes both real and imaginary components of the
+        signal. When False, only the real component is computed. Default is True.
+
     Example
     -------
 
@@ -146,6 +150,7 @@ class ConfigSimulator(Parseable):
     decompose_spectrum: Literal["none", "spin_system"] = "none"
     isotropic_interpolation: Literal["linear", "gaussian"] = "linear"
     custom_sampling: Optional[CustomSampling] = None
+    is_complex: bool = True
 
     class Config:
         extra = "forbid"

src/mrsimulator/simulator/tests/test_config.py

@@ -93,6 +93,7 @@ def test_config():
         "name": None,
         "description": None,
         "label": None,
+        "is_complex": True,
     }
 
     assert a.config.get_int_dict() == {
@@ -102,6 +103,7 @@ def test_config():
         "integration_volume": 1,
         "integration_density": 20,
         "isotropic_interpolation": 1,
+        "is_complex": True,
     }
 
     assert b != a
@@ -123,6 +125,7 @@ def test_config():
         "name": None,
         "description": None,
         "label": None,
+        "is_complex": True,
     }
 
     assert a.config.get_int_dict() == {
@@ -132,6 +135,7 @@ def test_config():
         "integration_volume": 2,
         "integration_density": 20,
         "isotropic_interpolation": 1,
+        "is_complex": True,
     }
 
     assert b != a