paper examples and bugfix in simulate

Author: jdiedrichsen

demos/demo_fmri_spm.ipynb

@@ -433,7 +433,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "env",
+   "display_name": "base",
    "language": "python",
    "name": "python3"
   },
@@ -447,7 +447,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.2"
+   "version": "3.11.5"
   },
   "orig_nbformat": 4
  },

demos/paper_examples/sim_crossval.ipynb

@@ -15,7 +15,7 @@ def crossval_sim(n_part=2,n_cond=4,n_sim=10,n_channel=200,sigma='iid'):
     Low numbers of partitions to emphasize increase in variance.
     """
 
-    cond_vec,part_vec = rsa.simulation.make_design(n_cond,n_part)
+    cond_vec,part_vec = pcm.sim.make_design(n_cond,n_part)
     true_dist = np.array([2,1,0,3,2,1])
     dist_type = np.array([1,2,3,4,5,6])
     D = sd.squareform(true_dist)

demos/paper_examples/sim_crossval.py

@@ -109,7 +109,7 @@ def make_dataset(model, theta, cond_vec, n_channel=30, n_sim=1,
     if noise_cov_trial is None:
         noise_chol_trial = None
     else:
-        if noise_cov_trial.shape != (n_channel, n_channel):
+        if noise_cov_trial.shape != (n_obs, n_obs):
             raise ValueError("noise covariance for trials needs to be \
                               n_obs x n_obs array")
         noise_chol_trial = np.linalg.cholesky(noise_cov_trial)
@@ -126,9 +126,9 @@ def make_dataset(model, theta, cond_vec, n_channel=30, n_sim=1,
     des = {"signal": signal, "noise": noise,
            "model": model.name, "theta": theta}
     dataset_list = []
-    for _ in range(0, n_sim):
+    for n in range(0, n_sim):
         # If necessary - make a new signal
-        if not use_same_signal:
+        if n==0 or not use_same_signal:
             true_U = make_signal(G, n_channel, use_exact_signal,
                                  signal_chol_channel)
         # Make noise with normal distribution