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Minor bug fixes #2

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merged 7 commits into from
Mar 30, 2015
Merged

Minor bug fixes #2

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8994f56
add both my changes and Dario's
keflavich Oct 20, 2014
5408e9f
adam's version of orion2scimes
keflavich Oct 21, 2014
92fa3b7
Merge branch 'master' of github.com:Astroua/scimes
keflavich Oct 21, 2014
39baa4e
bug fixes: imports primarily
keflavich Oct 21, 2014
af4bf93
remove comment
keflavich Oct 21, 2014
4b88b2d
Merge pull request #1 from Astroua/master
keflavich Nov 14, 2014
5a1584d
Merge branch 'master' of github.com:Astroua/scimes
adamginsburg Mar 30, 2015
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26 changes: 15 additions & 11 deletions scimes/orion2scimes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,9 @@
import numpy as np
import math
import aplpy
import random

from matplotlib import pyplot as plt

from astrodendro import Dendrogram, ppv_catalog
from astropy import units as u
Expand Down Expand Up @@ -64,13 +67,13 @@ def make_asgn(dendro, data_file, cores_idx = [], tag = '_', collapse = True):

# Making the assignment cube
if len(data.shape) == 3:
asgn = np.zeros(data.shape, dtype = int32)
asgn = np.zeros(data.shape, dtype = np.int32)

if len(data.shape) == 4:
asgn = np.zeros((data.shape[1],data.shape[2],data.shape[3]), dtype = int32)
asgn = np.zeros((data.shape[1],data.shape[2],data.shape[3]), dtype = np.int32)

for i in cores_idx:
asgn[where(d[i].get_mask(shape = asgn.shape))] = i
asgn[np.where(d[i].get_mask(shape = asgn.shape))] = i


# Write the fits file
Expand All @@ -85,8 +88,8 @@ def make_asgn(dendro, data_file, cores_idx = [], tag = '_', collapse = True):

asgn_map = np.amax(asgn.data, axis = 0)

matshow(asgn_map, origin = "lower")
colorbar()
plt.matshow(asgn_map, origin = "lower")
plt.colorbar()


return
Expand All @@ -95,13 +98,14 @@ def make_asgn(dendro, data_file, cores_idx = [], tag = '_', collapse = True):



path = '/Volumes/Zeruel_data/ORION/'
path = './'
#path = '/Volumes/Zeruel_data/ORION/'
#path = '/Users/Dario/Documents/dendrograms/'
filename = path+'orion'
filename = os.path.join(path, 'orion')

do_make = False
do_catalog = False
do_load = False
do_make = True
do_catalog = True
do_load = True


if do_make:
Expand All @@ -115,7 +119,7 @@ def make_asgn(dendro, data_file, cores_idx = [], tag = '_', collapse = True):
data = hdu.data
hd = hdu.header

if size(shape(data))==4:
if data.ndim==4:
data = data[0,:,:,:]


Expand Down
9 changes: 7 additions & 2 deletions scimes/scimes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,13 @@

from matplotlib import pyplot as plt

from sklearn.cluster import spectral_clustering
from itertools import combinations
from astrodendro import Dendrogram, ppv_catalog
from astropy import units as u
from astropy.stats import median_absolute_deviation as mad

from sklearn import metrics
from spectral import spectral_clustering
from skimage.measure import regionprops


def mat_smooth(Mat, scalpar = 0, lscal = False):
Expand Down
14 changes: 7 additions & 7 deletions scimes/spectral.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,13 +9,13 @@

import numpy as np

from ..base import BaseEstimator, ClusterMixin
from ..utils import check_random_state, as_float_array, deprecated
from ..utils.extmath import norm
from ..metrics.pairwise import pairwise_kernels
from ..neighbors import kneighbors_graph
from ..manifold import spectral_embedding
from .k_means_ import k_means
from sklearn.base import BaseEstimator, ClusterMixin
from sklearn.utils import check_random_state, as_float_array, deprecated
from sklearn.utils.extmath import norm
from sklearn.metrics.pairwise import pairwise_kernels
from sklearn.neighbors import kneighbors_graph
from sklearn.manifold import spectral_embedding
from sklearn.cluster.k_means_ import k_means


def discretize(vectors, copy=True, max_svd_restarts=30, n_iter_max=20,
Expand Down