From bda6d81710755ea4d5c9f7e3dc37f49e306c2889 Mon Sep 17 00:00:00 2001
From: Pierre-antoine Comby <pierre-antoine.comby@crans.org>
Date: Fri, 24 Nov 2023 17:35:38 +0100
Subject: [PATCH] add scenario1 as yaml.

---
 src/conf/reconstructors/zero_filled.yaml  |  2 +-
 src/conf/{experiments => }/scenario1.yaml | 13 ++++++++-----
 src/simfmri/analysis/stats.py             |  4 ++--
 src/simfmri/cli/main.py                   |  1 +
 4 files changed, 12 insertions(+), 8 deletions(-)
 rename src/conf/{experiments => }/scenario1.yaml (85%)

diff --git a/src/conf/reconstructors/zero_filled.yaml b/src/conf/reconstructors/zero_filled.yaml
index b273c9a..5fa4367 100644
--- a/src/conf/reconstructors/zero_filled.yaml
+++ b/src/conf/reconstructors/zero_filled.yaml
@@ -1 +1 @@
-- adjoint: {}
+adjoint: {}
diff --git a/src/conf/experiments/scenario1.yaml b/src/conf/scenario1.yaml
similarity index 85%
rename from src/conf/experiments/scenario1.yaml
rename to src/conf/scenario1.yaml
index e938dbb..c03019a 100644
--- a/src/conf/experiments/scenario1.yaml
+++ b/src/conf/scenario1.yaml
@@ -1,7 +1,7 @@
-# @package _global
-#
 # This files contains the configuration to reproduce the scenario 1 of the Simfmri paper.
 
+force_sim: false
+
 simulation:
   sim_params:
     sim_tr: 0.1
@@ -14,7 +14,7 @@ simulation:
   handlers:
     phantom-brainweb:
       subject_id: 5
-      bbox: [0.225,-0.07, 0.06, -0.055, None, None]
+      bbox: [0.225,-0.07, 0.06, -0.055, null, null]
     activation-block:
       event_name: block_on
       block_on: 20
@@ -25,15 +25,18 @@ simulation:
       snr: 100
     acquisition-vds:
       shot_time_ms: 50
-      acs: 0.125
+      acs: 1
       accel: 1
-      accel_axis: 1
+      accel_axis: 0
       constant: true
       direction: top-down
+      smaps: false
 
 reconstructors:
   adjoint: {}
 
+stats:
+  contrast_name: block_on
 
 
 hydra:
diff --git a/src/simfmri/analysis/stats.py b/src/simfmri/analysis/stats.py
index e2f300b..3d6dd00 100644
--- a/src/simfmri/analysis/stats.py
+++ b/src/simfmri/analysis/stats.py
@@ -56,8 +56,8 @@ def contrast_zscore(
         drift_model=sim.extra_infos.get("drift_model", None),
     )
     # Create a mask from reference data (not ideal, but best)
-    mask = sim.data_ref[0] > 0
-    image_ = abs(image)[:, mask]
+    mask = sim.static_vol > 0
+    image_ = abs(image)[..., mask].squeeze()
     logger.debug(f"image_={image_.shape}, design matrix={design_matrix.shape}")
     labels, results = run_glm(image_, design_matrix.values)
     # Translate formulas to vectors
diff --git a/src/simfmri/cli/main.py b/src/simfmri/cli/main.py
index f0d38d4..ffbe416 100644
--- a/src/simfmri/cli/main.py
+++ b/src/simfmri/cli/main.py
@@ -41,6 +41,7 @@ def main_app(cfg: DictConfig) -> None:
             simulator, sim = HandlerChain.from_conf(cfg.simulation)
             sim = simulator(sim)
             del simulator
+            os.makedirs(cache_dir, exist_ok=True)
             with open(sim_file, "wb") as f:
                 pickle.dump(sim, f)