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Load templates as memmap rather than in memory #167

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merged 8 commits into from
Apr 6, 2024
Merged

Load templates as memmap rather than in memory #167

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4570839
Load templates as memmap rather than in memory
DradeAW Feb 14, 2024
344f148
Templates as float32 for better memory/disk usage
DradeAW Feb 20, 2024
d80aa4c
Added option to not output the spike traces
DradeAW Feb 26, 2024
984e3c4
More memory-efficient load of templates
DradeAW Feb 26, 2024
37053f9
Memory improvement
DradeAW Feb 26, 2024
82c2e2d
Fixed wrong variables name in the docs
DradeAW Feb 29, 2024
7f72fba
Fixed `drift_times`
DradeAW Feb 29, 2024
f4c7dd8
Update src/MEArec/tools.py
alejoe91 Apr 6, 2024
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6 changes: 3 additions & 3 deletions src/MEArec/simulate_cells.py
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Original file line number Diff line number Diff line change
Expand Up @@ -875,7 +875,7 @@ def calc_extracellular(
if verbose >= 1:
print(f"Done generating EAPs for {cell_name}")

saved_eaps = np.array(saved_eaps)
saved_eaps = np.array(saved_eaps, dtype=np.float32)
saved_positions = np.array(saved_positions)
saved_rotations = np.array(saved_rotations)

Expand Down Expand Up @@ -1268,14 +1268,14 @@ def check_solidangle(matrix, pre, post, polarlim):
cell.set_rotation(x=x_rot, y=y_rot, z=z_rot)
rot = [x_rot, y_rot, z_rot]

lfp = electrodes.get_transformation_matrix() @ cell.imem
lfp = np.array(electrodes.get_transformation_matrix() @ cell.imem, dtype=np.float32)

# Reverse rotation to bring cell back into initial rotation state
if rotation is not None:
rev_rot = [-r for r in rot]
cell.set_rotation(rev_rot[0], rev_rot[1], rev_rot[2], rotation_order="zyx")

return 1000 * lfp, pos, rot, found_position
return 1e3 * lfp, pos, rot, found_position


def str2bool(v):
Expand Down
13 changes: 10 additions & 3 deletions src/MEArec/tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -213,7 +213,7 @@ def load_tmp_eap(templates_folder, celltypes=None, samples_per_cat=None, verbose
print("loading cell type: ", f)
if celltypes is not None:
if celltype in celltypes:
eaps = np.load(str(eaplist[idx]))
eaps = np.load(str(eaplist[idx]), mmap_mode="r")
locs = np.load(str(loclist[idx]))
rots = np.load(str(rotlist[idx]))

Expand All @@ -230,7 +230,7 @@ def load_tmp_eap(templates_folder, celltypes=None, samples_per_cat=None, verbose
else:
ignored_categories.add(celltype)
else:
eaps = np.load(str(eaplist[idx]))
eaps = np.load(str(eaplist[idx]), mmap_mode="r")
locs = np.load(str(loclist[idx]))
rots = np.load(str(rotlist[idx]))

Expand All @@ -245,10 +245,17 @@ def load_tmp_eap(templates_folder, celltypes=None, samples_per_cat=None, verbose
cat_list.extend([celltype] * samples_to_read)
loaded_categories.add(celltype)

if len(eap_list) > 0:
all_eaps = np.lib.format.open_memmap(templates_folder / "all_eaps.npy", mode="w+", dtype=eaps[0].dtype, shape=(len(eap_list), *eap_list[0].shape))
for i in range(len(eap_list)):
all_eaps[i, ...] = eap_list[i]
else:
all_eaps = np.array([])

if verbose:
print("Done loading spike data ...")

return np.array(eap_list), np.array(loc_list), np.array(rot_list), np.array(cat_list, dtype=str)
return all_eaps, np.array(loc_list), np.array(rot_list), np.array(cat_list, dtype=str)


def load_templates(templates, return_h5_objects=True, verbose=False, check_suffix=True):
Expand Down
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