· 6 years ago · Jan 17, 2020, 07:24 PM
1List of packages
2
3# Name Version Build Channel
4_libgcc_mutex 0.1 conda_forge conda-forge
5_openmp_mutex 4.5 0_gnu conda-forge
6_tflow_select 2.3.0 mkl
7absl-py 0.9.0 py37_0 conda-forge
8alabaster 0.7.12 py_0 conda-forge
9argh 0.26.2 py37_1001 conda-forge
10astor 0.7.1 py_0 conda-forge
11astroid 2.3.3 py37_1 conda-forge
12atomicwrites 1.3.0 py_0 conda-forge
13attrs 19.3.0 py_0 conda-forge
14autopep8 1.4.4 py_0 conda-forge
15babel 2.8.0 py_0 conda-forge
16backcall 0.1.0 py_0 conda-forge
17bleach 3.1.0 py_0 conda-forge
18bokeh 1.4.0 py37_0 conda-forge
19bzip2 1.0.8 h516909a_2 conda-forge
20c-ares 1.15.0 h516909a_1001 conda-forge
21ca-certificates 2019.11.28 hecc5488_0 conda-forge
22caiman 1.7.1 py37hb3f55d8_0 conda-forge
23cairo 1.16.0 hfb77d84_1002 conda-forge
24certifi 2019.11.28 py37_0 conda-forge
25cffi 1.13.2 py37h8022711_0 conda-forge
26chardet 3.0.4 py37_1003 conda-forge
27cloudpickle 1.2.2 py_1 conda-forge
28cryptography 2.8 py37h72c5cf5_1 conda-forge
29cycler 0.10.0 py_2 conda-forge
30cytoolz 0.10.1 py37h516909a_0 conda-forge
31dask-core 2.9.1 py_0 conda-forge
32dbus 1.13.6 he372182_0 conda-forge
33decorator 4.4.1 py_0 conda-forge
34defusedxml 0.6.0 py_0 conda-forge
35diff-match-patch 20181111 py_0 conda-forge
36docutils 0.16 py37_0 conda-forge
37entrypoints 0.3 py37_1000 conda-forge
38expat 2.2.5 he1b5a44_1004 conda-forge
39ffmpeg 4.1.3 h167e202_0 conda-forge
40flake8 3.7.9 py37_0 conda-forge
41fontconfig 2.13.1 h86ecdb6_1001 conda-forge
42freetype 2.10.0 he983fc9_1 conda-forge
43future 0.18.2 py37_0 conda-forge
44gast 0.2.2 py_0 conda-forge
45gettext 0.19.8.1 hc5be6a0_1002 conda-forge
46giflib 5.2.1 h516909a_1 conda-forge
47glib 2.58.3 py37h6f030ca_1002 conda-forge
48gmp 6.1.2 hf484d3e_1000 conda-forge
49gnutls 3.6.5 hd3a4fd2_1002 conda-forge
50google-pasta 0.1.8 py_0 conda-forge
51graphite2 1.3.13 hf484d3e_1000 conda-forge
52grpcio 1.23.0 py37he9ae1f9_0 conda-forge
53gst-plugins-base 1.14.5 h0935bb2_0 conda-forge
54gstreamer 1.14.5 h36ae1b5_0 conda-forge
55h5py 2.10.0 nompi_py37h513d04c_101 conda-forge
56harfbuzz 2.4.0 h9f30f68_3 conda-forge
57hdf5 1.10.5 nompi_h3c11f04_1104 conda-forge
58hdmf 1.5.3 py_0 conda-forge
59holoviews 1.12.7 py_0 conda-forge
60icu 64.2 he1b5a44_1 conda-forge
61idna 2.8 py37_1000 conda-forge
62imageio 2.6.1 py37_0 conda-forge
63imagesize 1.2.0 py_0 conda-forge
64importlib_metadata 1.4.0 py37_0 conda-forge
65intervaltree 3.0.2 py_0 conda-forge
66ipykernel 5.1.3 py37h5ca1d4c_0 conda-forge
67ipyparallel 6.2.4 py37_0 conda-forge
68ipython 7.11.1 py37h5ca1d4c_0 conda-forge
69ipython_genutils 0.2.0 py_1 conda-forge
70ipywidgets 7.5.1 py_0 conda-forge
71isort 4.3.21 py37_0 conda-forge
72jasper 1.900.1 h07fcdf6_1006 conda-forge
73jedi 0.14.1 py37_0 conda-forge
74jeepney 0.4.2 py_0 conda-forge
75jinja2 2.10.3 py_0 conda-forge
76joblib 0.14.1 py_0 conda-forge
77jpeg 9c h14c3975_1001 conda-forge
78jsonschema 3.2.0 py37_0 conda-forge
79jupyter 1.0.0 py_2 conda-forge
80jupyter_client 5.3.4 py37_1 conda-forge
81jupyter_console 6.0.0 py_0 conda-forge
82jupyter_core 4.6.1 py37_0 conda-forge
83keras-applications 1.0.8 py_1 conda-forge
84keras-preprocessing 1.1.0 py_0 conda-forge
85keyring 21.1.0 py37_0 conda-forge
86kiwisolver 1.1.0 py37hc9558a2_0 conda-forge
87lame 3.100 h14c3975_1001 conda-forge
88lazy-object-proxy 1.4.3 py37h516909a_0 conda-forge
89ld_impl_linux-64 2.33.1 h53a641e_7 conda-forge
90libblas 3.8.0 14_openblas conda-forge
91libcblas 3.8.0 14_openblas conda-forge
92libclang 9.0.1 default_hde54327_0 conda-forge
93libffi 3.2.1 he1b5a44_1006 conda-forge
94libgcc-ng 9.2.0 h24d8f2e_2 conda-forge
95libgfortran-ng 7.3.0 hdf63c60_4 conda-forge
96libgomp 9.2.0 h24d8f2e_2 conda-forge
97libiconv 1.15 h516909a_1005 conda-forge
98liblapack 3.8.0 14_openblas conda-forge
99liblapacke 3.8.0 14_openblas conda-forge
100libllvm9 9.0.1 hc9558a2_0 conda-forge
101libopenblas 0.3.7 h5ec1e0e_6 conda-forge
102libopencv 4.2.0 py37_1 conda-forge
103libpng 1.6.37 hed695b0_0 conda-forge
104libprotobuf 3.11.2 h8b12597_0 conda-forge
105libsodium 1.0.17 h516909a_0 conda-forge
106libspatialindex 1.9.3 he1b5a44_1 conda-forge
107libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
108libtiff 4.1.0 hc3755c2_3 conda-forge
109libuuid 2.32.1 h14c3975_1000 conda-forge
110libwebp 1.0.2 h56121f0_5 conda-forge
111libxcb 1.13 h14c3975_1002 conda-forge
112libxkbcommon 0.9.1 hebb1f50_0 conda-forge
113libxml2 2.9.10 hee79883_0 conda-forge
114lz4-c 1.8.3 he1b5a44_1001 conda-forge
115markdown 3.1.1 py_0 conda-forge
116markupsafe 1.1.1 py37h516909a_0 conda-forge
117matplotlib 3.1.2 py37_1 conda-forge
118matplotlib-base 3.1.2 py37h250f245_1 conda-forge
119mccabe 0.6.1 py_1 conda-forge
120mistune 0.8.4 py37h516909a_1000 conda-forge
121more-itertools 8.1.0 py_0 conda-forge
122mypy 0.761 py_0 conda-forge
123mypy_extensions 0.4.3 py37_0 conda-forge
124nbconvert 5.6.1 py37_0 conda-forge
125nbformat 5.0.3 py_0 conda-forge
126ncurses 6.1 hf484d3e_1002 conda-forge
127nettle 3.4.1 h1bed415_1002 conda-forge
128networkx 2.4 py_0 conda-forge
129nose 1.3.7 py37_1003 conda-forge
130notebook 6.0.1 py37_0 conda-forge
131nspr 4.24 he1b5a44_0 conda-forge
132nss 3.47 he751ad9_0 conda-forge
133numpy 1.17.3 py37h95a1406_0 conda-forge
134numpydoc 0.9.2 py_0 conda-forge
135olefile 0.46 py_0 conda-forge
136opencv 4.2.0 py37_1 conda-forge
137openh264 1.8.0 hdbcaa40_1000 conda-forge
138openssl 1.1.1d h516909a_0 conda-forge
139opt_einsum 3.1.0 py_0 conda-forge
140packaging 20.0 py_0 conda-forge
141pandas 0.25.3 py37hb3f55d8_0 conda-forge
142pandoc 2.9.1.1 0 conda-forge
143pandocfilters 1.4.2 py_1 conda-forge
144param 1.9.2 py_0 conda-forge
145parso 0.5.2 py_0 conda-forge
146pathtools 0.1.2 py_1 conda-forge
147pcre 8.43 he1b5a44_0 conda-forge
148peakutils 1.3.2 py_0 conda-forge
149pexpect 4.7.0 py37_0 conda-forge
150pickleshare 0.7.5 py37_1000 conda-forge
151pillow 7.0.0 py37hefe7db6_0 conda-forge
152pims 0.4.1 py_1 conda-forge
153pip 19.3.1 py37_0 conda-forge
154pixman 0.38.0 h516909a_1003 conda-forge
155pluggy 0.12.0 py_0 conda-forge
156prometheus_client 0.7.1 py_0 conda-forge
157prompt_toolkit 2.0.10 py_0 conda-forge
158protobuf 3.11.2 py37he1b5a44_0 conda-forge
159psutil 5.6.7 py37h516909a_0 conda-forge
160pthread-stubs 0.4 h14c3975_1001 conda-forge
161ptyprocess 0.6.0 py_1001 conda-forge
162py-opencv 4.2.0 py37h5ca1d4c_1 conda-forge
163pycodestyle 2.5.0 py_0 conda-forge
164pycparser 2.19 py37_1 conda-forge
165pydocstyle 5.0.2 py_0 conda-forge
166pyflakes 2.1.1 py_0 conda-forge
167pygments 2.5.2 py_0 conda-forge
168pylint 2.4.4 py37_0 conda-forge
169pynwb 1.1.2 py_0 conda-forge
170pyopenssl 19.1.0 py37_0 conda-forge
171pyparsing 2.4.6 py_0 conda-forge
172pyqt 5.12.3 py37hcca6a23_1 conda-forge
173pyqt5-sip 4.19.18 pypi_0 pypi
174pyqtgraph 0.11.0rc0 py_0 conda-forge
175pyqtwebengine 5.12.1 pypi_0 pypi
176pyrsistent 0.15.7 py37h516909a_0 conda-forge
177pysocks 1.7.1 py37_0 conda-forge
178python 3.7.6 h357f687_2 conda-forge
179python-dateutil 2.8.1 py_0 conda-forge
180python-jsonrpc-server 0.3.2 py_0 conda-forge
181python-language-server 0.31.4 py37_0 conda-forge
182pytz 2019.3 py_0 conda-forge
183pyviz_comms 0.7.2 py_0 conda-forge
184pywavelets 1.1.1 py37hc1659b7_0 conda-forge
185pyxdg 0.26 py_0 conda-forge
186pyyaml 5.3 py37h516909a_0 conda-forge
187pyzmq 18.1.1 py37h1768529_0 conda-forge
188qdarkstyle 2.7 py_0 conda-forge
189qt 5.12.5 hd8c4c69_1 conda-forge
190qtawesome 0.6.1 py_0 conda-forge
191qtconsole 4.6.0 py_0 conda-forge
192qtpy 1.9.0 py_0 conda-forge
193readline 8.0 hf8c457e_0 conda-forge
194requests 2.22.0 py37_1 conda-forge
195rope 0.16.0 py_0 conda-forge
196rtree 0.9.3 py37h7b0cdae_0 conda-forge
197ruamel.yaml 0.16.5 py37h516909a_1 conda-forge
198ruamel.yaml.clib 0.2.0 py37h516909a_0 conda-forge
199scikit-image 0.16.2 py37hb3f55d8_0 conda-forge
200scikit-learn 0.22.1 py37hcdab131_1 conda-forge
201scipy 1.4.1 py37h921218d_0 conda-forge
202secretstorage 3.1.2 py37_0 conda-forge
203send2trash 1.5.0 py_0 conda-forge
204setuptools 45.0.0 py37_1 conda-forge
205six 1.14.0 py37_0 conda-forge
206slicerator 1.0.0 py_0 conda-forge
207snowballstemmer 2.0.0 py_0 conda-forge
208sortedcontainers 2.1.0 py_0 conda-forge
209sphinx 2.3.1 py_0 conda-forge
210sphinxcontrib-applehelp 1.0.1 py_0 conda-forge
211sphinxcontrib-devhelp 1.0.1 py_0 conda-forge
212sphinxcontrib-htmlhelp 1.0.2 py_0 conda-forge
213sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
214sphinxcontrib-qthelp 1.0.2 py_0 conda-forge
215sphinxcontrib-serializinghtml 1.1.3 py_0 conda-forge
216spyder 4.0.1 py37_0 conda-forge
217spyder-kernels 1.8.1 py37_0 conda-forge
218sqlite 3.30.1 hcee41ef_0 conda-forge
219tensorboard 2.0.0 pyhb38c66f_1
220tensorflow 2.0.0 mkl_py37h66b46cc_0
221tensorflow-base 2.0.0 mkl_py37h9204916_0
222tensorflow-estimator 2.0.0 pyh2649769_0
223termcolor 1.1.0 py_2 conda-forge
224terminado 0.8.3 py37_0 conda-forge
225testpath 0.4.4 py_0 conda-forge
226tifffile 0.15.1 py37hc1659b7_1001 conda-forge
227tk 8.6.10 hed695b0_0 conda-forge
228toolz 0.10.0 py_0 conda-forge
229tornado 6.0.3 py37h516909a_0 conda-forge
230tqdm 4.41.1 py_0 conda-forge
231traitlets 4.3.3 py37_0 conda-forge
232typed-ast 1.4.1 py37h516909a_0 conda-forge
233typing_extensions 3.7.4.1 py37_0 conda-forge
234ujson 1.35 py37h516909a_1001 conda-forge
235urllib3 1.25.7 py37_0 conda-forge
236watchdog 0.9.0 py37_1 conda-forge
237wcwidth 0.1.8 py_0 conda-forge
238webencodings 0.5.1 py_1 conda-forge
239werkzeug 0.16.0 py_0 conda-forge
240wheel 0.33.6 py37_0 conda-forge
241widgetsnbextension 3.5.1 py37_0 conda-forge
242wrapt 1.11.2 py37h516909a_0 conda-forge
243wurlitzer 2.0.0 py37_0 conda-forge
244x264 1!152.20180806 h14c3975_0 conda-forge
245xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
246xorg-libice 1.0.10 h516909a_0 conda-forge
247xorg-libsm 1.2.3 h84519dc_1000 conda-forge
248xorg-libx11 1.6.9 h516909a_0 conda-forge
249xorg-libxau 1.0.9 h14c3975_0 conda-forge
250xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
251xorg-libxext 1.3.4 h516909a_0 conda-forge
252xorg-libxrender 0.9.10 h516909a_1002 conda-forge
253xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
254xorg-xextproto 7.3.0 h14c3975_1002 conda-forge
255xorg-xproto 7.0.31 h14c3975_1007 conda-forge
256xz 5.2.4 h14c3975_1001 conda-forge
257yaml 0.2.2 h516909a_1 conda-forge
258yapf 0.28.0 py_0 conda-forge
259zeromq 4.3.2 he1b5a44_2 conda-forge
260zipp 1.0.0 py_0 conda-forge
261zlib 1.2.11 h516909a_1006 conda-forge
262zstd 1.4.4 h3b9ef0a_1 conda-forge
263
264Output comments from python
265
266WHEN IMPORTING THE PACKAGES
267/usr/people/jmig/anaconda3/envs/caiman/lib/python3.7/site-packages/sklearn/utils/deprecation.py:144: FutureWarning: The sklearn.decomposition.incremental_pca module is deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.decomposition. Anything that cannot be imported from sklearn.decomposition is now part of the private API.
268 warnings.warn(message, FutureWarning)
269
270WHEN CREATING PARAMETERS OBJECT
271 72492 [params.py: set():888] [11492] Changing key fnames in group data from None to ['/usr/people/jmig/caiman_data/example_movies/Sue_2x_3000_40_-46.tif']
272 72494 [params.py: set():888] [11492] Changing key rf in group patch from None to 15
273 72496 [params.py: set():888] [11492] Changing key stride in group patch from None to 6
274 72499 [params.py: set():888] [11492] Changing key p in group preprocess from 2 to 1
275 72501 [params.py: set():888] [11492] Changing key nb in group init from 1 to 2
276 72503 [params.py: set():888] [11492] Changing key K in group init from 30 to 4
277 72505 [params.py: set():888] [11492] Changing key ssub in group init from 2 to 1
278 72508 [params.py: set():888] [11492] Changing key tsub in group init from 2 to 1
279 72510 [params.py: set():888] [11492] Changing key nb in group spatial from 1 to 2
280 72512 [params.py: set():888] [11492] Changing key p in group temporal from 2 to 1
281 72513 [params.py: set():888] [11492] Changing key nb in group temporal from 1 to 2
282 72514 [params.py: set():888] [11492] Changing key merge_thr in group merging from 0.8 to 0.85
283 72515 [params.py: set():888] [11492] Changing key min_SNR in group quality from 2.5 to 2.0
284 72520 [params.py: set():888] [11492] Changing key rval_thr in group quality from 0.8 to 0.85
285 72520 [params.py: set():888] [11492] Changing key min_cnn_thr in group quality from 0.9 to 0.99
286 72521 [params.py: set():888] [11492] Changing key min_SNR in group online from 2.5 to 2.0
287 72522 [params.py: set():888] [11492] Changing key rval_thr in group online from 0.8 to 0.85
288 72523 [params.py: set():888] [11492] Changing key strides in group motion from (96, 96) to (48, 48)
289 72524 [params.py: set():888] [11492] Changing key overlaps in group motion from (32, 32) to (24, 24)
290 72524 [params.py: set():888] [11492] Changing key pw_rigid in group motion from False to True
291
292WHEN PERFORMING MOTION CORRECTION
29384776 [movies.py: extract_shifts():371] [11492] Movie average is negative. Removing 1st percentile.
294 84778 [movies.py: extract_shifts():389] [11492] Movie average is negative. Removing 1st percentile.
295 84903 [movies.py: extract_shifts():371] [11492] Movie average is negative. Removing 1st percentile.
296 84906 [movies.py: extract_shifts():389] [11492] Movie average is negative. Removing 1st percentile.
297 85008 [movies.py: extract_shifts():371] [11492] Movie average is negative. Removing 1st percentile.
298 85010 [movies.py: extract_shifts():389] [11492] Movie average is negative. Removing 1st percentile.
299
300WHEN PERFORMING MEMORY MAPPING
301223008 [params.py: set():888] [7587] Changing key n_processes in group patch from 1 to 23
302 223010 [params.py: set():888] [7587] Changing key init_batch in group online from 200 to 3000
303 223012 [params.py: set():888] [7587] Changing key medw in group spatial from None to (3, 3)
304 223014 [params.py: set():888] [7587] Changing key n_pixels_per_process in group preprocess from None to 1256
305 223016 [params.py: set():888] [7587] Changing key n_pixels_per_process in group spatial from None to 1256
306 223018 [params.py: set():888] [7587] Changing key n_pixels_per_process in group preprocess from 1256 to 225
307 223020 [params.py: set():888] [7587] Changing key n_pixels_per_process in group spatial from 1256 to 225
308
309WHEN EXTRACTING deltaF/F VALUES
310 493286 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
311 493289 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
312 493291 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
313 493294 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
314 493297 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
315 493301 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
316 493305 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
317 493311 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
318 493320 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
319 493334 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
320 493355 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
321 493394 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
322 493468 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
323 493617 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
324 493922 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
325 494524 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
326 495723 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
327 498119 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
328 502908 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
329 512473 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.
330 531619 [stats.py: df_percentile():184] [7587] Percentile computation failed. Duplicating and trying again.