Skip to content

Tutorial notebook DAMP #920

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
NimaSarajpoor wants to merge 20 commits into
base: main
Choose a base branch
from
Open

Tutorial notebook DAMP #920

Changes from 1 commit
Commits
Show all changes
20 commits
Select commit Hold shift + click to select a range
b311533
Add tutorial notebook DAMP
NimaSarajpoor Oct 3, 2023
4ef1f5d
add function to compute range
NimaSarajpoor Oct 8, 2023
efeb68a
Clean code
NimaSarajpoor Oct 13, 2023
f3c7f30
enhance readability
NimaSarajpoor Oct 13, 2023
01bb14c
improve docstring
NimaSarajpoor Oct 14, 2023
f871b42
minor fix for finding dhunks for function
NimaSarajpoor Nov 6, 2023
d7d1314
improve docstring
NimaSarajpoor Nov 19, 2023
80f214e
minor fix in code and docstring
NimaSarajpoor Nov 19, 2023
d130159
add functions to complete DAMP
NimaSarajpoor Nov 19, 2023
d3d7e7d
minor enhancements
NimaSarajpoor Nov 19, 2023
50c6709
enhance code readability
NimaSarajpoor Nov 19, 2023
633cce8
Revise comments
NimaSarajpoor Nov 19, 2023
c112477
add performant func and minor enhancements
NimaSarajpoor Nov 26, 2023
585fc4c
add new example
NimaSarajpoor Nov 26, 2023
53f7346
minor fixes
NimaSarajpoor Nov 27, 2023
99593e0
minor fix to make sure chunks get updated in each iter
NimaSarajpoor Nov 29, 2023
5c110a1
use JIT compiled functions with fastmath flag where possible
NimaSarajpoor Dec 8, 2023
830bb27
Merge branch 'main' into DAMP
NimaSarajpoor Aug 18, 2025
4d87d99
fix code so that it becomes compatible with numpy>=2.0
NimaSarajpoor Aug 20, 2025
6b6e30f
Add new notebook to explore pyFFTW in DAMP
NimaSarajpoor Aug 20, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
minor fixes
  • Loading branch information
@NimaSarajpoor
NimaSarajpoor committed Nov 27, 2023
commit 53f73469d1385e6da98aad5e2a0fc119af224f38
77 changes: 35 additions & 42 deletions docs/Tutorial_DAMP.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 1,
"id": "c9564cff",
"metadata": {},
"outputs": [],
Expand All @@ -69,7 +69,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 18,
"id": "409dad09",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -128,14 +128,14 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 3,
"id": "c21c4587",
"metadata": {},
"outputs": [],
"source": [
"def next_pow2(val):\n",
" \"\"\"\n",
" Compute the smallest \"power of two\" number that is greater than/ equal to `v`\n",
" Compute the smallest \"power of two\" number that is greater than/ equal to `val`\n",
" \n",
" Parameters\n",
" ----------\n",
Expand All @@ -152,7 +152,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 19,
"id": "dd1f7b3d",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -214,15 +214,15 @@
" out.append([max(chunk_start, start), chunk_stop])\n",
" chunk_stop = chunk_start + m - 1\n",
" \n",
" if chunk_start <= 0:\n",
" if chunk_start <= start:\n",
" break\n",
" \n",
" return np.array(out)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 20,
"id": "5e45d72c",
"metadata": {},
"outputs": [
Expand All @@ -235,7 +235,7 @@
" [ 0, 56]])"
]
},
"execution_count": 6,
"execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -256,7 +256,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 6,
"id": "79663447",
"metadata": {},
"outputs": [],
Expand All @@ -269,8 +269,8 @@
" M_T, \n",
" Σ_T, \n",
" T_subseq_isconstant, \n",
" chunks_range,\n",
" bsf,\n",
" chunks_range=None,\n",
"):\n",
" \"\"\"\n",
" Compute the (approximate) distance between the subsequence `T[query_idx:query_idx+m]`\n",
Expand Down Expand Up @@ -300,13 +300,13 @@
" A numpy boolean array whose i-th element indicates whether the subsequence\n",
" `T[i : i+m]` is constant (True)\n",
" \n",
" bsf : float\n",
" The best-so-far discord distance\n",
" \n",
" chunks_range : numpy.ndarray, default None\n",
" chunks_range : numpy.ndarray\n",
" A 2D numpy array consisting of rows, each represents\n",
" the (start, stop) range of a chunk\n",
" \n",
" bsf : float\n",
" The best-so-far discord distance\n",
" \n",
" Returns\n",
" -------\n",
" nn_distance : float\n",
Expand All @@ -316,11 +316,6 @@
" bsf : float\n",
" The best-so-far discord distance \n",
" \"\"\"\n",
" if chunks_range is None:\n",
" # The avoid the trivial (left) neighbors of `T[query_idx : query_idx+m]`,\n",
" # the stop index of non-trivial subsequences is `query_idx - excl_zone + m`\n",
" chunks_range = naive_get_range_damp(query_idx - excl_zone + m, m, start=0)\n",
" \n",
" nn_distance = np.inf\n",
" for (start, stop) in chunks_range:\n",
" QT = core.sliding_dot_product(\n",
Expand Down Expand Up @@ -350,7 +345,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 21,
"id": "c76317b5",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -429,7 +424,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 32,
"id": "769bddad",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -470,7 +465,6 @@
" \n",
" excl_zone = int(math.ceil(m / stumpy.core.config.STUMPY_EXCL_ZONE_DENOM))\n",
" chunks_range = get_damp_range(split_idx - excl_zone + m, m, start=0)\n",
" \n",
" last_chunk_size = chunks_range[-1, 1] - chunks_range[-1, 0]\n",
" last_chunk_size_cutoff = next_pow2(last_chunk_size)\n",
" \n",
Expand All @@ -487,14 +481,13 @@
" excl_zone, \n",
" M_T, \n",
" Σ_T, \n",
" T_subseq_isconstant, \n",
" bsf, \n",
" chunks_range=chunks_range\n",
" T_subseq_isconstant, \n",
" chunks_range,\n",
" bsf,\n",
" )\n",
" _foreward_process(T, m, excl_zone, M_T, Σ_T, T_subseq_isconstant, i, lookahead, PL)\n",
" \n",
" chunks_range = chunks_range + 1 \n",
" # make a decision on whether to create new chunk or not for the subsequence [0, m]\n",
" chunks_range[:] = chunks_range + 1 \n",
" if last_chunk_size < last_chunk_size_cutoff:\n",
" chunks_range[-1, 0] = 0 \n",
" last_chunk_size += 1\n",
Expand All @@ -521,7 +514,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 23,
"id": "2cfbc771",
"metadata": {},
"outputs": [],
Expand All @@ -536,7 +529,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 24,
"id": "a935f31f",
"metadata": {},
"outputs": [
Expand All @@ -546,7 +539,7 @@
"text": [
"discord_dist: 8.500883427933504\n",
"discord_index: 209\n",
"running time [sec]: 5.248243093490601\n"
"running time [sec]: 4.881464958190918\n"
]
}
],
Expand All @@ -566,7 +559,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 25,
"id": "2b461592",
"metadata": {},
"outputs": [
Expand All @@ -576,7 +569,7 @@
"text": [
"discord_dist: 8.500883427933504\n",
"discord_index: 209\n",
"running time [sec]: 2.2584328651428223\n"
"running time [sec]: 2.2210960388183594\n"
]
}
],
Expand Down Expand Up @@ -605,7 +598,7 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 26,
"id": "d8e9fa63",
"metadata": {},
"outputs": [],
Expand All @@ -620,7 +613,7 @@
},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": 27,
"id": "263bca9c",
"metadata": {},
"outputs": [
Expand All @@ -630,7 +623,7 @@
"text": [
"discord_dist: 7.606279752022369\n",
"discord_index: 8109\n",
"running time [sec]: 5.100044012069702\n"
"running time [sec]: 4.996989965438843\n"
]
}
],
Expand All @@ -651,7 +644,7 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 28,
"id": "78d09bda",
"metadata": {},
"outputs": [
Expand All @@ -661,7 +654,7 @@
"text": [
"discord_dist: 7.606279752022363\n",
"discord_index: 8109\n",
"running time [sec]: 6.70897912979126\n"
"running time [sec]: 6.67956805229187\n"
]
}
],
Expand Down Expand Up @@ -690,7 +683,7 @@
},
{
"cell_type": "code",
"execution_count": 16,
"execution_count": 33,
"id": "6d64f488",
"metadata": {},
"outputs": [],
Expand All @@ -705,7 +698,7 @@
},
{
"cell_type": "code",
"execution_count": 17,
"execution_count": 34,
"id": "159e03dc",
"metadata": {},
"outputs": [
Expand All @@ -715,7 +708,7 @@
"text": [
"discord_dist: 29.42331306408431\n",
"discord_index: 6110\n",
"running time [sec]: 5.572257995605469\n"
"running time [sec]: 5.483174085617065\n"
]
}
],
Expand All @@ -736,7 +729,7 @@
},
{
"cell_type": "code",
"execution_count": 18,
"execution_count": 35,
"id": "9ef28e10",
"metadata": {},
"outputs": [
Expand All @@ -746,7 +739,7 @@
"text": [
"discord_dist: 29.423313064084333\n",
"discord_index: 6110\n",
"running time [sec]: 55.545814990997314\n"
"running time [sec]: 55.60335397720337\n"
]
}
],
Expand Down