Update Ralph/LISA work in calmarg

.github/workflows/ci.yml

@@ -134,6 +134,27 @@ jobs:
       - name: Run simulation_manager smoke test
         run: bash .travis/test-simulation-manager.sh
 
+  lisa-check:
+    needs: install
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+          cache: 'pip'
+          cache-dependency-path: requirements.txt
+      - name: Enable symlink
+        run: sudo ln -sf $(which python3) /usr/bin/python
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip --break-system-packages
+          python -m pip install -r requirements.txt --break-system-packages
+          python -m pip install coverage pytest --break-system-packages
+          python -m pip install --editable . --break-system-packages
+      - name: Run LISA smoke and contract tests
+        run: bash .travis/test-lisa.sh
+
   integration-check:
     needs: install
     runs-on: ubuntu-latest

.travis/test-lisa.sh

@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+PYTHON_BIN="${RIFT_LISA_PYTHON:-${PYTHON:-python}}"
+if ! command -v "${PYTHON_BIN}" >/dev/null 2>&1; then
+  PYTHON_BIN="$(command -v python3)"
+fi
+
+"${PYTHON_BIN}" -m pytest -q \
+  MonteCarloMarginalizeCode/Code/test/test_lisa_auxiliary_imports.py \
+  MonteCarloMarginalizeCode/Code/test/test_lisa_response_import.py \
+  MonteCarloMarginalizeCode/Code/test/test_lisa_lalsimutils_compat.py \
+  MonteCarloMarginalizeCode/Code/test/test_lisa_run_checks.py \
+  MonteCarloMarginalizeCode/Code/test/test_lisa_demo_contract.py \
+  MonteCarloMarginalizeCode/Code/test/test_lisa_helper_contract.py \
+  MonteCarloMarginalizeCode/Code/test/test_lisa_pseudo_pipe_contract.py \
+  MonteCarloMarginalizeCode/Code/test/test_lisa_pp_surface.py \
+  MonteCarloMarginalizeCode/Code/test/test_lisa_synthetic_demo.py

MonteCarloMarginalizeCode/Code/RIFT/LISA/initial_grid/__init__.py

@@ -0,0 +1 @@
+"""Initial-grid helpers for LISA analyses."""

MonteCarloMarginalizeCode/Code/RIFT/LISA/initial_grid/fisher_errors.py

@@ -0,0 +1,264 @@
+#!/usr/bin/env python
+
+"""The purpose of this code is to give rough estimates of width of posteriors for Mc, eta, spin and skylocation for initial grid generation."""
+import numpy as np
+import RIFT.lalsimutils as lsu
+from RIFT.LISA.response.LISA_response import *
+from argparse import ArgumentParser
+from scipy.interpolate import interp1d
+import os
+
+__author__ = "A. Jan"
+###########################################################################################
+# Functions to generate 2-PN waveforms as per http://arxiv.org/abs/gr-qc/9502040.
+###########################################################################################
+def amplitude_2PN(fvals, Mc):
+    """Returns amplitude in frequency domains for a 2-PN waveform"""
+#    print(f"amplitude_2PN: {locals()}")
+    return 1 * Mc**(5/6) * fvals**(-7/6)
+
+def phase_2PN(fvals, Mc, eta, sigma, beta, coa_phase=0, coa_time=0):
+    """Returns phase in frequency domains for a 2-PN waveform"""
+#    print(f"phase_2PN: {locals()}")
+    M = Mc/eta**(3/5)
+    fac = np.pi*M*fvals
+    newtonian = 3/128 * (np.pi*Mc*fvals)**(-5/3)
+    one_PN = 20/9 * (743/336 + 11/4* eta)*(fac)**(2/3)
+    one_five_PN = 4 * (4*np.pi - beta)*fac
+    two_PN = 10*(3058673/1016064 + 5429/1008*eta + 617/144*eta**2 - sigma)*(fac)**(4/3)
+    phase_vals = 2*np.pi*fvals*coa_time - coa_phase - np.pi/4 + newtonian * (1 + one_PN  - one_five_PN + two_PN)
+    return phase_vals
+
+def time_2PN(fvals, Mc, eta, sigma, beta, coa_time=0):
+    """Returns time corresponding to input frequency for a 2-PN waveform"""
+    M = Mc/eta**(3/5)
+    fac = np.pi*M*fvals
+    time_vals = coa_time - 5/256* Mc*(np.pi*Mc*fvals)**(-8/3) * (1 + 4/3 * (743/336 + 11/4 * eta)*(fac)**(2/3) - 8/5 *(4*np.pi - beta)*fac + 2*(3058673/1016064 + 5429/1008 * eta + 617/144*eta**2 - sigma)*(fac)**(4/3))
+    return time_vals
+
+def get_sigma_beta(Mc, eta, a1z, a2z):
+    """Returns sigma and beta parameters that are used in construction of the waveform. These parameters contain information about spin."""
+    alpha = Mc / eta**(3/5)
+    beta = Mc**2 / eta**(1/5)
+    m1 = 0.5 * (alpha + np.sqrt(alpha**2 - 4*beta))
+    m2 = 0.5 * (alpha - np.sqrt(alpha**2 - 4*beta))
+    M = m1 + m2
+    sigma_val = eta/48 * (-247 * a1z*a1z + 721 * a1z*a2z)
+    beta_val = 1/12 * ((113 * (m1/M)**2 + 75 * eta)*a1z + (113 * (m2/M)**2 + 75 * eta)*a2z )
+    return sigma_val, beta_val
+
+def get_derivative(fvals, Mc, eta, sigma, beta, wf):
+    """Derivates of the waveform with respect to coalescence time, coalescence phase, Mc, eta, sigma, beta"""
+#    print(f"get_derivative: {locals()}")
+    M = Mc/eta**(3/5)
+    v = (np.pi*M*fvals)**(1/3)
+
+    A4 = 4/3 * (743/336 + 11/4 * eta)
+    B4 = 8/5 * (4*np.pi - beta)
+    C4 = 2 * (3058673/1016064 + 5429/1008 * eta + 617/144 * eta**2 - sigma)
+
+    A5 = 743/168 - 33/4 * eta
+    B5 = 27/5 * (4*np.pi - beta)
+    C5 = 18 * (3058673/1016064 - 5429/4032 * eta - 617/96*eta**2 -  sigma)
+
+    d_tc = 2*np.pi*1j*(fvals) * wf
+    d_phi = -1j * wf
+
+    d_log_mc =   -1j*(5/128 * (np.pi*Mc*fvals)**(-5/3) * (1 + A4*v**2 - B4*v**3 + C4*v**4)) * wf
+    d_log_eta =  -1j*(1/96  * (np.pi*Mc*fvals)**(-5/3) * (    A5*v**2 - B5*v**3 + C5*v**4)) * wf
+
+    d_beta = 1j * 3/32 * eta**(-3/5) * (np.pi*Mc*fvals)**(-2/3) * wf
+    d_sigma = -1j * 15/64 * eta**(-4/5) * (np.pi*Mc*fvals)**(-1/3) * wf
+    return np.array([d_tc, d_phi, d_log_mc, d_log_eta, d_beta, d_sigma])
+
+def get_wf(fvals, Mc, eta, sigma, beta, psd_vals, coa_phase=0, coa_time=0, snr=None, LISA_response=False, skylocation = None):
+    """Generate a 2-PN waveform"""
+    phase = phase_2PN(fvals, Mc, eta, sigma, beta, coa_phase, coa_time)
+    amp = amplitude_2PN(fvals, Mc)
+    wf = amp * np.exp(1j*phase)
+    if LISA_response:
+         H = transformed_Hplus_Hcross(skylocation[0], skylocation[1], 0.0, 0.0, 0.0, 2, 2)
+         time = time_2PN(fvals, Mc, eta, sigma, beta, coa_time)
+         A, E, T = Evaluate_Gslr(time + coa_time, fvals, H, skylocation[0], skylocation[1])
+         wf = wf * A
+    if snr:
+        # bring the source closer or further, depending on SNR
+        deltaF = np.diff(fvals)[0]
+        snr_fiducial = np.sqrt(get_inner_product(wf, wf, psd_vals, deltaF))
+        correction = snr / snr_fiducial
+        wf = correction * wf
+    return wf
+
+###########################################################################################
+# Utilities
+###########################################################################################
+def load_psd(psdf, fvals):
+    """Loads in PSD"""
+    # load in psd
+    psd_dict = {}
+    inst = "A"
+    print( "Reading PSD for instrument %s from %s" % (inst, psdf))
+    psd_dict[inst] = lsu.get_psd_series_from_xmldoc(psdf, inst)
+    psd_fvals = psd_dict[inst].f0 + psd_dict[inst].deltaF*np.arange(psd_dict[inst].data.length)
+    interp_func = interp1d(psd_fvals, psd_dict[inst].data.data)
+    return interp_func(fvals)
+
+def get_mass_from_mc_eta(mc, eta):
+    """Returns m1, m2 from mc and eta."""
+    alpha = mc / eta**(3/5)
+    beta = mc**2 / eta**(1/5)
+    m1 = 0.5 * (alpha + np.sqrt(alpha**2 - 4*beta))
+    m2 = 0.5 * (alpha - np.sqrt(alpha**2 - 4*beta))
+    return m1, m2
+
+def get_mc_eta_from_mass(m1, m2):
+    """Returns m1, m2 from mc and eta."""
+    mc = (m1*m2)**(3/5) / (m1+m2)**(1/5)
+    eta = (m1*m2) / (m1+m2)**(2)
+    if eta==0.25:
+        eta=0.24999
+    return mc, eta
+
+def get_inner_product(wf1, wf2, psd_vals, deltaF):
+    """Calculate inner product"""
+    assert len(wf1) == len(wf2) == len(psd_vals)
+    weight = 1/psd_vals
+    intgd = np.sum(np.conj(wf1) * wf2 * weight) * deltaF
+    return 4 * np.real(intgd)
+
+def get_massratio_error(eta, q, eta_error):
+    return eta_error * (1 + q)**3 / (1 - q)
+
+def get_spin_error(eta, q, a1z, a2z, eta_error, beta_error, sigma_error):
+    q_error = get_massratio_error(eta, q, eta_error)
+    if round(a1z,4)==round(a2z,4):
+        a1z = a1z + 0.001 * a1z
+        a2z = a2z - 0.001 * a2z
+
+    c1 = sigma_error - eta_error/48 * (474*a1z*a2z)
+    a1 = eta/48 * 474 * a2z
+    b1 = eta/48 * 474 * a1z
+
+    c2 = beta_error - eta_error/12 * ( (113/q + 75)*a1z + (113*q + 75)*a2z) - eta/12 * ( (-113/q**2)*a1z*q_error + 113*a2z*q_error)
+    a2 = eta/12 * (113/q + 75)
+    b2 = eta/12 * (113*q + 75)
+
+    coefficients = np.array([ [a1, a2], [b1, b2] ])
+    dependents = np.array( [c1, c2] )
+    answers = np.abs(np.linalg.solve(coefficients, dependents))
+    return [np.min(answers), np.max(answers)]
+
+###########################################################################################
+# Fisher matrix
+###########################################################################################
+def get_fisher_matrix(Mc, eta, sigma, beta, fvals, psd_vals, deltaF, wf):
+    """Get fisher information matrix"""
+    derivatives = get_derivative(fvals, Mc, eta, sigma, beta, wf)
+    N = 6
+    tau_ij = np.zeros((N,N))
+    for i in np.arange(0, N):
+        for j in np.arange(0, N):
+            tau_ij[i,j] = get_inner_product(derivatives[i], derivatives[j], psd_vals, deltaF)
+    inv_tau_ij = (np.linalg.inv(tau_ij))
+    return tau_ij, inv_tau_ij
+
+def get_error_bounds(P_inj, snr, psd_path, snr_fmin=0.0001):
+    """Get error bounds on parameters using fisher information matrix."""
+    response=True # use LISA response
+    deltaF = 0.00001 # hardcoded deltaF
+    mc, eta = get_mc_eta_from_mass(P_inj.m1/lsu.lsu_MSUN, P_inj.m2/lsu.lsu_MSUN)
+    q = P_inj.m2/P_inj.m1
+
+    if q == 1:
+        q = 0.9
+
+    # convert chirp mass to seconds
+    Mc = mc * 5 * 10**(-6)
+    M = Mc/eta**(3/5)
+    sigma, beta = get_sigma_beta(Mc, eta, P_inj.s1z, P_inj.s2z)
+    fmax = 6**(-3/2) / np.pi/ M
+    print(f"Fmax is = {fmax} Hz")
+    fvals = np.arange(float(snr_fmin), fmax, deltaF)
+
+    # Load psd
+    psd_vals = load_psd(psd_path, fvals)
+
+    # generate waveform
+    wf = get_wf(fvals, Mc, eta, sigma, beta, psd_vals, 0, float(P_inj.tref), snr=float(snr), LISA_response=response, skylocation=[P_inj.theta, P_inj.phi])
+    print(f"SNR of generated waveform is = {np.sqrt(get_inner_product(wf,wf,psd_vals, deltaF))}")
+
+    # Calculate fisher matrix
+    tau_ij, inv_tau_ij = get_fisher_matrix(Mc, eta, sigma, beta, fvals, psd_vals, deltaF, wf)
+    if eta < 0.24:
+        factor_eta = 12.5
+    if eta >=0.24: # the errors estimates seem to be large for q~1 case.
+        factor_eta = 1.0
+    factor_mc = 50
+    factor_spin1 = 60
+    factor_spin2 = 60
+    spin_bounds = get_spin_error(eta, q, P_inj.s1z, P_inj.s2z, (np.sqrt(1/tau_ij[3,3]))*eta, np.sqrt(1/tau_ij[4,4]), np.sqrt(1/tau_ij[5,5]))
+
+    print(f"Mc span = {2*factor_mc*np.sqrt(1/tau_ij[2,2])*mc}, eta span = {2*np.sqrt(1/tau_ij[3,3])*eta*factor_eta}, s1z span = {2*factor_spin1*spin_bounds[0]}, s2z span = {2*factor_spin2*spin_bounds[1]}, beta span = {0.036*(210/snr)**2}, lambda span = {0.044*(210/snr)**2}")
+
+
+    return np.array([ mc - factor_mc*np.sqrt(1/tau_ij[2,2])*mc, mc + factor_mc*np.sqrt(1/tau_ij[2,2])*mc, eta-(np.sqrt(1/tau_ij[3,3]))*eta*factor_eta, eta+(np.sqrt(1/tau_ij[3,3]))*eta*factor_eta, P_inj.s1z - factor_spin1*spin_bounds[0], P_inj.s1z + factor_spin1*spin_bounds[0], P_inj.s2z - factor_spin2*spin_bounds[1],  P_inj.s2z + factor_spin2*spin_bounds[1], P_inj.theta - 0.018*(210/snr), P_inj.theta + 0.018*(210/snr),  P_inj.phi - 0.022*(210/snr), P_inj.phi + 0.022*(210/snr)])
+
+
+###########################################################################################
+
+if __name__ =='__main__':
+    ###########################################################################################
+    parser=ArgumentParser()
+    parser.add_argument("--inj", help="Full path to mdc.xml.gz")
+    parser.add_argument("--psd-path", help="Full path to A-psd.xm.gz")
+    parser.add_argument("--snr", help="SNR of the signal")
+    parser.add_argument("--snr-fmin", help="fmin used in snr calculations", default=0.0001)
+    parser.add_argument("--generate-grid", help="Use the fisherbounds to generate grid", default=True)
+    parser.add_argument("--points", help="number of points in the grid", default=25000)
+    opts = parser.parse_args()
+    print(f"Loading file:\n {opts.inj}")
+    P_inj_list = lsu.xml_to_ChooseWaveformParams_array(opts.inj)
+    P_inj = P_inj_list[0]
+    print("######")
+    print(f"m1 = {P_inj.m1/lsu.lsu_MSUN}, m2 = {P_inj.m2/lsu.lsu_MSUN}, s1z = {P_inj.s1z}, s2z = {P_inj.s2z}, beta = {P_inj.theta}, lambda = {P_inj.phi}, tref = {P_inj.tref} s")
+    print("######")
+    error_bounds = get_error_bounds(P_inj, float(opts.snr), opts.psd_path, snr_fmin=opts.snr_fmin)
+    print(f"Mc bounds = [{error_bounds[0]:0.2f}, {error_bounds[1]:0.2f}]")
+    print(f"eta bounds = [{error_bounds[2]:0.8f}, {error_bounds[3]:0.8f}]")
+    print(f"s1z bounds = [{error_bounds[4]:0.6f}, {error_bounds[5]:0.6f}]")
+    print(f"s2z bounds = [{error_bounds[6]:0.6f}, {error_bounds[7]:0.6f}]")
+    print(f"beta bounds = [{error_bounds[8]:0.6f}, {error_bounds[9]:0.6f}]")
+    print(f"lambda bounds = [{error_bounds[10]:0.6f}, {error_bounds[11]:0.6f}]")
+    mc_span, eta_span = (error_bounds[1] - error_bounds[0]), (error_bounds[3] - error_bounds[2])
+    s1z_span, s2z_span =  (error_bounds[5] - error_bounds[4]), (error_bounds[7] - error_bounds[6])
+    beta_span, lambda_span =  (error_bounds[9] - error_bounds[8]), (error_bounds[11] - error_bounds[10])
+    if opts.generate_grid:
+        import os
+        from RIFT.LISA.utils.utils import *
+        cmd = f"util_ManualOverlapGrid.py --inj {opts.inj} "
+        cmd += f"--parameter mc --parameter-range '[{error_bounds[0]:0.2f}, {error_bounds[1]:0.2f}]' "
+        cmd += f"--parameter eta --parameter-range '[{error_bounds[2]:0.5f}, {error_bounds[3]:0.5f}]' "
+        cmd += f"--random-parameter s1z --random-parameter-range '[{error_bounds[4]:0.6f}, {error_bounds[5]:0.6f}]' "
+        cmd += f"--random-parameter s2z --random-parameter-range '[{error_bounds[6]:0.6f}, {error_bounds[7]:0.6f}]' "
+        cmd += f"--random-parameter theta --random-parameter-range '[{error_bounds[8]:0.6f}, {error_bounds[9]:0.6f}]' "
+        cmd += f"--random-parameter phi --random-parameter-range '[{error_bounds[10]:0.6f}, {error_bounds[11]:0.6f}]' "
+        cmd += f"--grid-cartesian-npts {int(opts.points)} --skip-overlap"
+        print(f"\t Generating grid\n{cmd}")
+        os.system(cmd)
+        os.system('mv overlap-grid.xml.gz overlap-grid-primary.xml.gz')
+
+        secondary_peak = get_secondary_mode_for_skylocation(float(P_inj.tref), P_inj.phi, P_inj.theta)
+        beta_sec, lambda_sec = secondary_peak[0,2], secondary_peak[0,1]
+        print(f"Secondary peak: lambda {lambda_sec}, beta {beta_sec}")
+        cmd = f"util_ManualOverlapGrid.py --inj {opts.inj} "
+        cmd += f"--parameter mc --parameter-range '[{error_bounds[0]:0.2f}, {error_bounds[1]:0.2f}]' "
+        cmd += f"--parameter eta --parameter-range '[{error_bounds[2]:0.5f}, {error_bounds[3]:0.5f}]' "
+        cmd += f"--random-parameter s1z --random-parameter-range '[{error_bounds[4]:0.6f}, {error_bounds[5]:0.6f}]' "
+        cmd += f"--random-parameter s2z --random-parameter-range '[{error_bounds[6]:0.6f}, {error_bounds[7]:0.6f}]' "
+        cmd += f"--random-parameter theta --random-parameter-range '[{beta_sec-0.5*beta_span}, {beta_sec+0.5*beta_span}]' "
+        cmd += f"--random-parameter phi --random-parameter-range '[{lambda_sec-0.5*lambda_span}, {lambda_sec+0.5*lambda_span}]' "
+        cmd += f"--grid-cartesian-npts {int(opts.points)} --skip-overlap"
+        print(f"\t Generating grid\n{cmd}")
+        os.system(cmd)
+        os.system('mv overlap-grid.xml.gz overlap-grid-secondary.xml.gz')
+        os.system('ligolw_add overlap-grid-primary.xml.gz overlap-grid-secondary.xml.gz -o overlap-grid.xml.gz')