From b3dc2153a27119e60903440e3c917f4245cbf852 Mon Sep 17 00:00:00 2001
From: Baptiste Bauvin <baptiste.bauvin@lis-lab.fr>
Date: Fri, 25 Mar 2022 07:42:35 -0400
Subject: [PATCH] Feat ids
---
summit/multiview_platform/utils/dataset.py | 57 +++++++++++-----------
1 file changed, 29 insertions(+), 28 deletions(-)
diff --git a/summit/multiview_platform/utils/dataset.py b/summit/multiview_platform/utils/dataset.py
index 2a33b34b..15175976 100644
--- a/summit/multiview_platform/utils/dataset.py
+++ b/summit/multiview_platform/utils/dataset.py
@@ -14,7 +14,7 @@ from .organization import secure_file_path
of SuMMIT'''
-class Dataset():
+class Dataset:
"""
This is the base class for all the type of multiview datasets of SuMMIT.
"""
@@ -165,11 +165,9 @@ class Dataset():
return selected_label_names
- def gen_feat_id(self):
- self.feature_ids = [["ID_" + str(i) for i in
+ def gen_feat_id(self, view_ind):
+ self.feature_ids[view_ind] = ["ID_" + str(i) for i in
range(self.get_v(view_ind).shape[1])]
- for view_ind in self.view_dict.values()]
-
class RAMDataset(Dataset):
@@ -193,13 +191,14 @@ class RAMDataset(Dataset):
self.name = name
self.nb_view = len(self.views)
self.is_temp = False
- if feature_ids is not None:
- feature_ids = [[feature_id if not is_just_number(feature_id)
- else "ID_" + feature_id for feature_id in
- feat_ids] for feat_ids in feature_ids]
- self.feature_ids = feature_ids
- else:
- self.gen_feat_id()
+ self.feature_ids = [_ for _ in range(self.nb_view)]
+ for view_ind in range(self.nb_view):
+ if feature_ids is not None:
+ self.feature_ids[view_ind] = [feature_id if not is_just_number(feature_id)
+ else "ID_" + feature_id for feature_id in
+ feature_ids[view_ind]]
+ else:
+ self.gen_feat_id(view_ind)
def get_view_name(self, view_idx):
return self.view_names[view_idx]
@@ -377,14 +376,15 @@ class HDF5Dataset(Dataset):
else:
self.sample_ids = ["ID_" + str(i)
for i in range(labels.shape[0])]
- if feature_ids is not None:
- feature_ids = [[feature_id if not is_just_number(feature_id)
- else "ID_" + feature_id for feature_id in
- feat_ids] for feat_ids in feature_ids]
- self.feature_ids = feature_ids
- else:
- self.gen_feat_id()
-
+ self.feature_ids = [_ for _ in range(self.nb_view)]
+ for view_index in range(self.nb_view):
+ if feature_ids is not None:
+ feat_ids = [feature_id if not is_just_number(feature_id)
+ else "ID_" + feature_id for feature_id in
+ feature_ids[view_index]]
+ self.feature_ids = feat_ids
+ else:
+ self.gen_feat_id(view_index)
def get_v(self, view_index, sample_indices=None):
""" Extract the view and returns a numpy.ndarray containing the description
@@ -443,6 +443,7 @@ class HDF5Dataset(Dataset):
"""
self.nb_view = self.dataset["Metadata"].attrs["nbView"]
+ self.feature_ids = [_ for _ in range(self.nb_view)]
self.view_dict = self.get_view_dict()
self.view_names = [self.dataset["View{}".format(ind)].attrs['name'] for ind in range(self.nb_view)]
if "sample_ids" in self.dataset["Metadata"].keys():
@@ -454,14 +455,14 @@ class HDF5Dataset(Dataset):
else:
self.sample_ids = ["ID_" + str(i) for i in
range(self.dataset["Labels"].shape[0])]
- if "feature_ids" in self.dataset["Metadata"].keys():
- self.feature_ids = [[feature_id.decode()
- if not is_just_number(feature_id.decode())
- else "ID_" + feature_id.decode()
- for feature_id in feature_ids] for feature_ids in
- self.dataset["Metadata"]["feature_ids"]]
- else:
- self.gen_feat_id()
+ for view_index in range(self.nb_view):
+ if "feature_ids-View{}".format(view_index) in self.dataset["Metadata"].keys():
+ self.feature_ids[view_index] = [feature_id.decode()
+ if not is_just_number(feature_id.decode())
+ else "ID_" + feature_id.decode()
+ for feature_id in self.dataset["Metadata"]["feature_ids-View{}".format(view_index)]]
+ else:
+ self.gen_feat_id(view_index)
def get_nb_samples(self):
"""
--
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