def main():
"""
Entry point for analysis
"""
noise_type = "gaussian" if ARGS.use_noisy_lowres else "none"
# load both RSM types and covert to RDMs
hires_rsms = load_rsms(glm_dir="GLM_vanilla")
lowres_rsms = load_rsms(glm_dir="GLM_vanilla_sim2pt4", noise_type=noise_type)
hires_rdms = {partition: 1 - x for (partition, x) in hires_rsms.items()}
lowres_rdms = {partition: 1 - x for (partition, x) in lowres_rsms.items()}
# get pandas dataframe
data = prepare_dataframe(hires_rdms, lowres_rdms)
# report on mean per data source
hires_data = data[data.data_srcs == 0]
lowres_data = data[data.data_srcs == 1]
print("Hires RDM Magnitude vs. Lowres")
report_ttest_2_sample(
hires_data.magnitudes, lowres_data.magnitudes, print_mean_var=True
)
# run analysis of variance
fpath = f"{PATHS['r_scripts']}/data/mean_abs_rdm.csv"
data.to_csv(fpath)
subprocess.call(
f"Rscript --vanilla {PATHS['r_scripts']}/mean_abs_rdm_script.r {fpath}",
shell=True,
)
def get_partition_weights(
thresh="thr_75",
glm_dir="GLM_vanilla",
metric=PRIMARY_METRIC,
r2_control=False,
noise_type="none",
):
rsms = load_rsms(
thresh=thresh,
glm_dir=glm_dir,
r2_control=r2_control,
metric=metric,
noise_type=noise_type,
)
rdms = {partition: 1 - x for (partition, x) in rsms.items()}
regressors = build_regressors()
# fit domain, category, and depth weights to each rdm
partition_weights = {}
for partition in PARTITIONS:
partition_rdms = rdms[partition]
weights_list = []
for rdm in partition_rdms:
lower_tri_rdm = get_lower_tri(rdm, with_diagonal=True)
weights = fit_rdm(lower_tri_rdm, regressors, method="lsq")
weights_list.append(weights)
partition_weights[partition] = np.stack(weights_list)
return partition_weights
def get_partition_weights(
thresh="thr_75", glm_dir="GLM_vanilla", r2_control=False, noise_type="none"
):
rsms = load_rsms(
thresh=thresh, glm_dir=glm_dir, r2_control=r2_control, noise_type=noise_type
)
rdms_by_depth = {
partition: np.array([1 - split_by_depth(rsm) for rsm in partition_rsms])
for (partition, partition_rsms) in rsms.items()
}
regressors = build_regressors()
partition_weights = {}
for partition in PARTITIONS:
partition_rdms = rdms_by_depth[partition]
subject_weights = []
for subject_rdms in partition_rdms:
depth_weights = []
for depth_rdm in subject_rdms:
weights = fit_rdm(
get_lower_tri(depth_rdm, with_diagonal=True),
regressors,
method="lsq",
)
depth_weights.append(weights)
subject_weights.append(np.stack(depth_weights))
partition_weights[partition] = np.stack(subject_weights)
return partition_weights
def main():
"""
Entry point for analysis
"""
rsms = load_rsms()
rdms = {partition: 1 - x for (partition, x) in rsms.items()}
intersubject_corr_dict = {}
for partition_name, partition_rdms in rdms.items():
lower_tris = np.array([
get_lower_tri(subject_rdm, with_diagonal=True)
for subject_rdm in partition_rdms
])
lower_tri_corrs = np.corrcoef(lower_tris)
# reduce symmetric corrmat by taking lower triangle (without diagonal)
pairwise_intersubject_corrs = get_lower_tri(lower_tri_corrs)
intersubject_corr_dict[partition_name] = pairwise_intersubject_corrs
print(f"Mean intersub RDM corr in {partition_name}")
report_ttest_1_sample(pairwise_intersubject_corrs, print_mean_var=True)
print(f"Lateral vs. medial difference")
report_ttest_2_sample(intersubject_corr_dict["VTC_lateral"],
intersubject_corr_dict["VTC_medial"])
def make_plots(glm_dir, save_dir):
"""
Entry point for script
"""
rsm_plot_params = {
"beta": {"cmap": plot_utils.blueblackred, "clim": [0, 1]},
"tnorm": {"cmap": plot_utils.blueblackred, "clim": [0, 1]},
"tstat": {"cmap": plot_utils.blueblackred, "clim": [-0.5, 0.5]},
"zscore": {"cmap": plot_utils.blueblackred, "clim": [-0.5, 0.5]},
"znorm": {"cmap": plot_utils.blueblackred, "clim": [-0.5, 0.5]},
"betasub": {"cmap": plot_utils.blueblackred, "clim": [-0.5, 0.5]},
}
rdm_plot_params = {
"beta": {"cmap": plot_utils.blueblackred, "clim": [0, 1]},
"tnorm": {"cmap": plot_utils.blueblackred, "clim": [0, 1]},
"tstat": {"cmap": plot_utils.blueblackred, "clim": [0.5, 1.5]},
"zscore": {"cmap": plot_utils.blueblackred, "clim": [0.5, 1.5]},
"znorm": {"cmap": plot_utils.blueblackred, "clim": [0.5, 1.5]},
"betasub": {"cmap": plot_utils.blueblackred, "clim": [0.5, 1.5]},
}
key_order = ["znorm", "tstat", "zscore", "betasub", "tnorm", "beta"]
for metric in key_order:
print(f"Plotting metric: {metric}")
rsms = load_rsms(metric=metric, glm_dir=glm_dir)
mds_anchor = get_MDS_anchor(rsms)
mean_rsms = {}
mean_rdms = {}
for rsm_name, rsm in rsms.items():
mean_rsms[rsm_name] = np.mean(rsm, axis=0, keepdims=True)
mean_rdms[rsm_name] = np.mean(1 - rsm, axis=0, keepdims=True)
# align the group-average RSMs to the mds anchor
aligned_embeddings = plot_utils.embed_rsms(
mean_rsms, alignment_anchor=mds_anchor
)
plot_helper(
mean_rdms,
aligned_embeddings,
rdm_plot_params[metric],
f"{save_dir}/{metric}_rdms.png",
)
plot_helper(
mean_rsms,
aligned_embeddings,
rsm_plot_params[metric],
f"{save_dir}/{metric}_rsms.png",
)
def main():
"""
Entry point for script
"""
save_dir = f"{PATHS['figures']}/figure_8af_rdms_by_depth"
mkdirquiet(save_dir)
# define some colormaps and limits here for each metric (maybe move to constants?)
plot_params = {
"tstat": {"cmap": plot_utils.blueblackred, "clim": [0.5, 1.5]},
"zscore": {"cmap": plot_utils.blueblackred, "clim": [0.5, 1.5]},
"znorm": {"cmap": plot_utils.blueblackred, "clim": [0.5, 1.5]},
}
for metric in plot_params.keys():
print(f"Plotting metric: {metric}")
rsms = load_rsms(metric=metric)
mean_rdms_by_depth = {
partition: np.mean(
[1 - split_by_depth(rsm) for rsm in partition_rsms], axis=0
)
for (partition, partition_rsms) in rsms.items()
}
base = 6
fig, axes = plt.subplots(figsize=(base * 3, base * 2), nrows=2, ncols=3)
for partition_idx, partition in enumerate(PARTITIONS):
if partition == "hOc1":
continue
rdm_dict = {
f"{partition}_{x}": mean_rdms_by_depth[partition][x] for x in range(3)
}
plot_utils.plot_rdms(
axes[partition_idx, :],
rdm_dict,
cmap=plot_params[metric]["cmap"],
clim=plot_params[metric]["clim"],
)
savefig(f"{save_dir}/{metric}.png")
plt.close(fig)
def get_partition_weights(glm_dir="GLM_vanilla", noise_type="none"):
rsms = load_rsms(glm_dir=glm_dir, noise_type=noise_type)
rdms_by_depth = {
partition:
np.array([1 - split_by_depth(rsm) for rsm in partition_rsms])
for (partition, partition_rsms) in rsms.items()
}
# fit domain, category, and depth weights to each rdm
partition_weights = {}
for partition in PARTITIONS:
partition_rdms = rdms_by_depth[partition]
subject_weights = []
for subject_rdms in partition_rdms:
depth_weights = []
for depth_rdm in subject_rdms:
domain_weights_list = []
for domain_idx in range(5):
start = domain_idx * 2
end = start + 2
domain_rdm = depth_rdm[start:end, start:end]
within_category_mean = np.mean(
(domain_rdm[0, 0], domain_rdm[1, 1]))
between_category_mean = np.mean(
(domain_rdm[0, 1], domain_rdm[1, 0]))
domain_weights_list.append(
[within_category_mean, between_category_mean])
depth_weights.append(np.stack(domain_weights_list))
subject_weights.append(np.stack(depth_weights))
partition_weights[partition] = np.stack(subject_weights)
return partition_weights
def main():
"""
Entry point for analysis
"""
rsms = load_rsms()
rdms = {name: 1 - rsm for (name, rsm) in rsms.items()}
partition_pairs = {
"lateral-medial": ["VTC_lateral", "VTC_medial"],
"lateral-V1": ["VTC_lateral", "hOc1"],
"medial-V1": ["VTC_medial", "hOc1"],
}
pair_corrs = {}
for name, pair in partition_pairs.items():
rdms_a = rdms[pair[0]]
rdms_b = rdms[pair[1]]
subject_corrs = []
for a, b in zip(rdms_a, rdms_b):
lower_tri_a = get_lower_tri(a)
lower_tri_b = get_lower_tri(b)
corr = np.corrcoef(np.stack((lower_tri_a, lower_tri_b)))[0, 1]
subject_corrs.append(corr)
print(f"\nCorrelations between {pair[0]} and {pair[1]}")
pair_corrs[name] = np.array(subject_corrs)
report_ttest_1_sample(np.array(subject_corrs), print_mean_var=True)
print(f"\nt-test between lateral-medial and lateral-V1")
report_ttest_2_sample(pair_corrs["lateral-medial"],
pair_corrs["lateral-V1"])
print(f"\nt-test between lateral-medial and medial-V1")
report_ttest_2_sample(pair_corrs["lateral-medial"],
pair_corrs["medial-V1"])
def main():
"""
Entry point for analysis
"""
rsms = load_rsms()
compute_reliability_full(rsms)