From 923715d1652c533ef206121d4b9d529a1ac72252 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Fri, 18 Feb 2022 17:25:00 +0000
Subject: [PATCH] add grouper dir and file asserts
---
compiler.py | 79 +++++++++++++++++++++++++++++++++++++----------
core/processor.py | 9 +++++-
grouper.py | 5 ++-
3 files changed, 74 insertions(+), 19 deletions(-)
diff --git a/compiler.py b/compiler.py
index aa7af166..e1eb93c5 100644
--- a/compiler.py
+++ b/compiler.py
@@ -8,11 +8,27 @@ Main dataframe structure
# dir = "/home/alan/Documents/dev/skeletons/data/2021_06_15_pypipeline_unit_test_00/2021_06_15_pypipeline_unit_test_00/"
# dir = "/home/alan/Documents/dev/libs/aliby/data/2021_08_24_2Raf_00/2021_08_24_2Raf_00/"
dirs = [
- "/home/alan/Documents/dev/skeletons/data/2021_08_24_2Raf_00/2021_08_24_2Raf_00"
+ # "2019_07_16_aggregates_CTP_switch_2_0glu_0_0glu_URA7young_URA8young_URA8old_01/",
+ # "2020_10_01_exp_00/",
+ # "2020_10_02_downUpshift_twice_2_0_2_glu_ura8_phluorinMsn2_phluorinMig1_01/",
+ # "/home/alan/Documents/dev/skeletons/data/2021_05_27_PDR5Fluc_00/2021_05_27_PDR5Fluc_00/",
+ # "2020_10_22_downUpshift_2_0_2_glu_dual_phluorin__glt1_psa1_ura7__thrice_00/",
+ # "2021_06_15_pypipeline_unit_test_00/",
+ # "2021_06_27_ph_calibration_dual_phl_ura8_5_04_5_83_7_69_7_13_6_59__01/",
+ # "/home/alan/Documents/dev/skeletons/data/2021_08_24_2Raf_00/2021_08_24_2Raf_00",
+ # "/home/alan/Documents/dev/skeletons/data/2021_09_15_1_Raf_06/2021_09_15_1_Raf_06/"
# "/home/alan/Documents/dev/libs/aliby/data/sofia/2021_08_24_2Raf_00/2021_08_24_2Raf_00",
# "/home/alan/Documents/dev/libs/aliby/data/sofia/2021_09_15_1_Raf_06/2021_09_15_1_Raf_06",
# "/home/alan/Documents/dev/libs/aliby/data/sofia/2021_09_17_0_1_Raf_00/2021_09_17_0_1_Raf_00",
+ # "/home/alan/Documents/dev/skeletons/data/2021_09_15_1_Raf_06/2021_09_15_1_Raf_06/",
+ # "/home/alan/Documents/dev/skeletons/data/2021_08_24_2Raf_00/2021_08_24_2Raf_00/",
+ # "/home/alan/Documents/dev/skeletons/data/2021_11_01_01_Raf_00/2021_11_01_01_Raf_00/",
+ "/home/alan/Documents/dev/skeletons/data/2020_10_23_downUpshift_2_0_2_glu_dual_phluorin__glt1_psa1_ura7__twice__04/2020_10_23_downUpshift_2_0_2_glu_dual_phluorin__glt1_psa1_ura7__twice__04"
+ # "/home/alan/Documents/dev/skeletons/data/2021_11_05_wt_bs2_bs3_00/2021_11_05_wt_bs2_bs3_00/"
]
+# outdir = "/home/alan/Documents/dev/skeletons/data"
+# dirs = Path(outdir).glob("*ph*")
+
import h5py
from abc import abstractclassmethod, abstractmethod
@@ -361,23 +377,34 @@ class PageOrganiser(object):
if yloc is None:
yloc = slice(0, self.gs.nrows)
- return func(
- *args,
- ax=self.fig.add_subplot(self.gs[xloc, yloc]),
- **kwargs,
- )
+ if not isinstance(func, list):
+ func = [func]
+
+ for f in func:
+ f(
+ *args,
+ ax=self.fig.add_subplot(self.gs[xloc, yloc]),
+ **kwargs,
+ )
def plot(self):
instructions: Iterable[Dict[str, Union[str, Iterable]]] = (
+ # [
{
"data": "slice",
- "func": "stripplot",
- "args": ("count", "group"),
- "kwargs": {
- "hue": None,
- },
+ "func": "barplot",
+ "args": ("ntraps", "position"),
+ "kwargs": {"hue": "group", "palette": "muted"},
"loc": (0, 0),
},
+ # {
+ # "data": "slice",
+ # "func": "barplot",
+ # "args": ("ntraps", "position"),
+ # "kwargs": {"hue": "group", "palette": "muted"},
+ # "loc": (0, 0),
+ # },
+ # ],
{
"data": "delta_traps",
"func": "barplot",
@@ -440,12 +467,15 @@ class PageOrganiser(object):
# for dir in dirs:
# print(f"Compiling {dir}")
-# fullpath = Path("/home/alan/Documents/dev/skeletons/data/") / dir / dir
-# compiler = ExperimentCompiler(None, fullpath)
-# tmp = compiler.run()
-# po = PageOrganiser(tmp, grid_spec=(3, 2))
-# po.plot()
-# po.save(fullpath / f"{dir.rstrip('/')}_report.pdf")
+# try:
+# fullpath = Path("/home/alan/Documents/dev/skeletons/data/") / dir / dir
+# compiler = ExperimentCompiler(None, fullpath)
+# tmp = compiler.run()
+# po = PageOrganiser(tmp, grid_spec=(3, 2))
+# po.plot()
+# po.save(fullpath / f"{dir.rstrip('/')}_report.pdf")
+# except Exception as e:
+# print(e)
#### Live editing
@@ -484,3 +514,18 @@ import numpy as np
# # for i in range(2):
# # axes[i].plot(signal[:, i])
# # plt.show()
+
+# f, ax = plt.subplots(figsize=(6, 15))
+# df = df.sort_values("group")
+# sns.barplot(data=df, x="ntraps", y="position", hue="group", palette="pastel")
+# sns.set_color_codes("muted")
+# sns.barplot(data=df, x="count", y="position", hue="group", palette="muted")
+# plt.show()
+
+# fpath = "/home/alan/Documents/dev/skeletons/data/2019_07_16_aggregates_CTP_switch_2_0glu_0_0glu_URA7young_URA8young_URA8old_01/2019_07_16_aggregates_CTP_switch_2_0glu_0_0glu_URA7young_URA8young_URA8old_01/URA7_young001.h5"
+# with h5py.File(fpath, "r") as f:
+# x, y = zip(*f["trap_info/trap_locations"][()])
+
+# plt.scatter(x, y)
+# plt.show()
+# sns.heatmap()
diff --git a/core/processor.py b/core/processor.py
index 7548a65e..0d7707fa 100644
--- a/core/processor.py
+++ b/core/processor.py
@@ -70,7 +70,6 @@ class PostProcessorParameters(ParametersABC):
[
"/extraction/general/None/volume",
"/postprocessing/savgol/extraction_general_None_volume",
- # "/postprocessing/bud_metric/extraction_general_None_volume",
],
],
[
@@ -78,9 +77,17 @@ class PostProcessorParameters(ParametersABC):
[
"/extraction/general/None/volume",
"/postprocessing/dsignal/postprocessing_savgol_extraction_general_None_volume",
+ "/postprocessing/savgol/extraction_general_None_volume",
+ # "/postprocessing/gpsignal/postprocessing_savgol_extraction_general_None_volume/growthrate",
"/postprocessing/dsignal/extraction_general_None_volume",
],
],
+ [
+ "dsignal",
+ [
+ "/postprocessing/bud_metric/extraction_general_None_volume",
+ ],
+ ],
[
"aggregate",
[
diff --git a/grouper.py b/grouper.py
index 57f6c69f..f16b410a 100644
--- a/grouper.py
+++ b/grouper.py
@@ -19,7 +19,10 @@ class Grouper(ABC):
files = []
def __init__(self, dir):
- self.files = list(Path(dir).glob("*.h5"))
+ path = Path(dir)
+ assert path.exists(), "Dir does not exist"
+ self.files = list(path.glob("*.h5"))
+ assert len(self.files), "No valid h5 files in dir"
self.load_signals()
def load_signals(self):
--
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