Merge pull request #76 from MingjieJian/develop

docs(driver_guide): renew ordinary driver_guide
MingjieJian · Jul 14, 2024 · 229332b · 229332b
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diff --git a/docs/driver_guide/abfind.md b/docs/driver_guide/abfind.md
@@ -3,65 +3,67 @@
 Suppose we have a list of lines (stored as as a DataFrame called `linelist`) with their measured EW as follow (appended to the line list as the last column):
 
 ```
-	wavelength	id	EP	loggf	C6	D0	EW
-0	11032.103	12.0	5.9460	-1.801	0.000	NaN	23.05
-1	11033.662	12.0	5.9460	-2.073	0.000	NaN	13.33
-2	11034.481	12.0	5.9460	-2.426	0.000	NaN	6.24
-3	11005.127	14.0	6.2228	-2.098	-7.200	NaN	5.54
-4	11013.703	14.0	6.2061	-0.983	-7.320	NaN	48.24
-5	11017.966	14.0	6.2061	0.760	-7.320	NaN	281.02
-6	11040.405	14.0	6.2061	-1.449	-7.320	NaN	22.53
-7	11019.848	19.0	2.6700	-0.010	3073.329	NaN	11.13
-8	11022.653	19.0	2.6703	-0.161	3073.329	NaN	7.98
-9	11015.530	24.0	3.4493	-0.429	-7.530	NaN	43.10
-10	11044.610	24.0	3.0112	-1.930	-7.780	NaN	5.74
-11	11013.235	26.0	4.7955	-1.383	-7.550	NaN	35.22
-12	11026.788	26.0	3.9434	-2.805	-7.810	NaN	11.92
-13	11045.599	26.0	5.5870	-0.624	-7.500	NaN	35.73
-14	11057.772	26.0	4.8349	-1.967	-7.550	NaN	11.55
-15	11069.374	26.0	6.2223	-1.055	-7.140	NaN	5.06
-16	11081.595	26.0	5.6425	-1.419	-7.470	NaN	7.37
-17	11088.584	28.0	4.1647	-1.512	-7.560	NaN	16.36
-18	11054.253	30.0	5.7958	-0.300	0.000	NaN	18.43
+       wavelength    id     EP  loggf    C6  D0      EW
+85992    8002.576  26.0  4.580 -1.618 -7.79 NaN   22.80
+86381    8026.940  14.0  6.261 -1.004 -6.98 NaN   34.24
+86400    8027.941  26.0  3.252 -2.785 -7.73 NaN   28.46
+86401    8028.313  26.0  4.473 -0.686 -7.54 NaN   76.66
+86520    8035.618  14.0  5.984 -1.372 -7.16 NaN   24.95
+86696    8046.047  26.0  4.415 -0.100 -7.55 NaN  125.55
+86735    8047.617  26.0  0.859 -4.742 -7.85 NaN   50.73
+86750    8049.366  14.0  6.269 -1.287 -6.98 NaN   20.15
+87069    8071.283  14.0  6.099 -1.192 -7.06 NaN   31.16
+87075    8072.164  26.0  2.424 -3.519 -7.82 NaN   32.43
+87105    8073.028  14.0  6.274 -1.381 -6.98 NaN   16.29
+87158    8075.150  26.0  0.915 -5.088 -7.85 NaN   30.34
+87245    8080.545  26.0  3.301 -2.710 -7.73 NaN   29.76
+87316    8085.172  26.0  4.446 -0.121 -7.55 NaN  121.43
+87399    8089.354  26.0  5.067 -1.141 -7.73 NaN   23.30
+87433    8093.232  14.0  5.863 -1.075 -7.19 NaN   47.38
+87518    8096.875  26.0  4.076 -1.767 -7.80 NaN   37.74
 ```
 
 ```{note}
 The DataFrame has to be sorted in id and wavelength.
 ```
 
+This line list can be loaded using:
+
+```py
+ges_linelist = pymoog.line_data.read_linelist('ges')
+ges_linelist = ges_linelist[(ges_linelist['wavelength'] > 8000) & (ges_linelist['wavelength'] < 8100) & (ges_linelist['EW'] > 15)]
+ges_linelist = ges_linelist[(ges_linelist['id'] == 26) | (ges_linelist['id'] == 14)]
+ges_linelist
+```
+
 Then abfind can run as:
 ```py
-a = pymoog.abfind.abfind(5000, 4.0, 0.0, line_list=linelist)
+a = pymoog.abfind.abfind(5777, 4.0, 0, line_list=ges_linelist)
 a.prepare_file()
 a.run_moog()
 a.read_output()
 ```
 The output of abfind, `a.abfind_res` will be stored as a dict with it keys as elements and values as DataFrame:
 ```
-{12.0:    wavelength    ID     EP  logGF   EWin  logRWin  abund  delavg
- 0   11032.103  12.0  5.946 -1.801  23.05   -5.680  7.376  -0.002
- 1   11033.662  12.0  5.946 -2.073  13.33   -5.918  7.378   0.000
- 2   11034.481  12.0  5.946 -2.426   6.24   -6.248  7.379   0.001,
- 14.0:    wavelength    ID     EP  logGF    EWin  logRWin  abund  delavg
- 0   11005.127  14.0  6.223 -2.098    5.54   -6.298  7.606  -0.030
- 1   11013.703  14.0  6.206 -0.983   48.24   -5.359  7.639   0.003
- 2   11017.966  14.0  6.206  0.760  281.02   -4.593  7.667   0.031
- 3   11040.405  14.0  6.206 -1.449   22.53   -5.690  7.632  -0.004,
- 19.0:    wavelength    ID    EP  logGF   EWin  logRWin  abund  delavg
- 0   11019.848  19.0  2.67 -0.010  11.13   -5.996  4.866  -0.002
- 1   11022.653  19.0  2.67 -0.161   7.98   -6.140  4.871   0.002,
- 24.0:    wavelength    ID     EP  logGF   EWin  logRWin  abund  delavg
- 0    11015.53  24.0  3.449 -0.429  43.10   -5.408  5.044   0.002
- 1    11044.61  24.0  3.011 -1.930   5.74   -6.284  5.040  -0.002,
- 26.0:    wavelength    ID     EP  logGF   EWin  logRWin  abund  delavg
- 0   11013.235  26.0  4.795 -1.383  35.22   -5.495  7.129  -0.076
- 1   11026.788  26.0  3.943 -2.805  11.92   -5.966  7.046  -0.159
- 2   11045.599  26.0  5.587 -0.624  35.73   -5.490  7.242   0.037
- 3   11057.772  26.0  4.835 -1.967  11.55   -5.981  7.171  -0.033
- 4   11069.374  26.0  6.222 -1.055   5.06   -6.340  7.359   0.154
- 5   11081.595  26.0  5.643 -1.419   7.37   -6.177  7.282   0.077,
- 28.0:    wavelength    ID     EP  logGF   EWin  logRWin  abund  delavg
- 0   11088.584  28.0  4.165 -1.512  16.36   -5.831  6.009     0.0}
+{14.0:    wavelength    ID     EP  logGF   EWin  logRWin  abund  delavg
+ 0    8071.283  14.0  6.099 -1.192  31.16   -5.413  7.497   0.016
+ 1    8026.940  14.0  6.261 -1.004  34.24   -5.370  7.509   0.027
+ 2    8035.618  14.0  5.984 -1.372  24.95   -5.508  7.448  -0.033
+ 3    8049.366  14.0  6.269 -1.287  20.15   -5.601  7.504   0.023
+ 4    8093.232  14.0  5.863 -1.075  47.38   -5.233  7.432  -0.049
+ 5    8073.028  14.0  6.274 -1.381  16.29   -5.695  7.497   0.016,
+ 26.0:     wavelength    ID     EP  logGF    EWin  logRWin  abund  delavg
+ 0     8089.354  26.0  5.067 -1.141   23.30   -5.541  7.387   0.053
+ 1     8085.172  26.0  4.446 -0.121  121.43   -4.823  7.266  -0.068
+ 2     8080.545  26.0  3.301 -2.710   29.76   -5.434  7.376   0.042
+ 3     8075.150  26.0  0.915 -5.088   30.34   -5.425  7.373   0.039
+ 4     8002.576  26.0  4.580 -1.618   22.80   -5.545  7.387   0.053
+ 5     8047.617  26.0  0.859 -4.742   50.73   -5.200  7.293  -0.041
+ 6     8046.047  26.0  4.415 -0.100  125.55   -4.807  7.271  -0.063
+ 7     8028.313  26.0  4.473 -0.686   76.66   -5.020  7.238  -0.096
+ 8     8027.941  26.0  3.252 -2.785   28.46   -5.450  7.380   0.046
+ 9     8072.164  26.0  2.424 -3.519   32.43   -5.396  7.361   0.027
+ 10    8096.875  26.0  4.076 -1.767   37.74   -5.332  7.340   0.006}
 ```
 
 ![](../img/driver_guide/abfind.png)
diff --git a/docs/driver_guide/binary.md b/docs/driver_guide/binary.md
@@ -0,0 +1,10 @@
+# binary
+
+```py
+b = pymoog.binary.binary([[5777, 4, 0], [5777, 2, 0]], 10540, 10600, 50000, line_list='vald_3000_24000')
+b.prepare_file(deltaradvel=10.5, lumratio=1)
+b.run_moog()
+b.read_spectra()
+```
+
+Using `plt.plot(b.wav, b.flux)`:
diff --git a/docs/driver_guide/blends.md b/docs/driver_guide/blends.md
@@ -1,17 +1,18 @@
 # blends: force-fitting abundances to match blended-line equivalent widths
 
 Blends driver fit the EW of a feature as a whole, only varing the abunance specified. 
-The following example shows a fitting of Fe abundance of the feature from 10817.7 to 10818.9A, with an observed EW of 80mA.
+The following example shows a fitting of Fe abundance of the feature from 8002.076 to 8003.076A, with an observed EW of 38.76mA.
 
 ```py
-b = pymoog.blends.blends(5000, 4.0, 0, 10817.7, 10818.9, 80, 26, line_list='vald_3000_24000')
+b = pymoog.blends.blends(5777, 4.0, 0, 8002.576-0.5, 8002.576+0.5, 38.76, 26)
 b.prepare_file()
 b.run_moog()
 b.read_output()
-b.blends_s_df
 ```
 
+The result is sotred in `b.blends_s_df`:
+
 ```py
-wavelength	ID	EP	logGF	EWin	logRWin	abund	delavg
-0	10818.275	26.0	3.96	-1.948	80.0	-5.131	7.325	0.0
+   wavelength    ID    EP  logGF   EWin  logRWin  abund  delavg
+0    8002.576  26.0  4.58 -1.618  38.76   -5.315  7.706     0.0
 ```
diff --git a/docs/driver_guide/cog.md b/docs/driver_guide/cog.md
@@ -5,15 +5,24 @@ The `cog` driver generate the curve-of-growth for individual line.
 Let’s look at a Si line with following parameters (and stored in file `use.list`):
 
 ```
-wavelength	id	EP	loggf	C6	D0	EW
-0	11040.405	14.0	6.2061	-1.449	-7.32	NaN	22.53
+     wavelength    id     EP  loggf    C6  D0  EW
+1001    9122.791  20.0  6.001 -4.956 -6.55 NaN NaN
 ```
 
+This line can be loaded by:
+
 ```py
-c = pymoog.cog.cog(5000, 4.0, 0, line_list=MOOG_run_path+'use.list')
+vald = pymoog.line_data.read_linelist('vald_winered')
+use_list = vald.loc[1001:1001]
+```
+
+```py
+c = pymoog.cog.cog(5000, 4, 0, line_list=use_list)
 c.prepare_file()
 c.run_moog()
 c.read_output()
 ```
 
+The result is sotred in `c.loggf` and `c.logrw`.
+
 ![](../img/driver_guide/cog.png)
diff --git a/docs/driver_guide/weedout.md b/docs/driver_guide/weedout.md
@@ -3,13 +3,35 @@
 It is sometimes useful to remove the weak lines which do not affect the spectra so much, keeping the line list short and clean.
 The `weedout` driver is for this task.
 
+After `w.read_linelist`, the strong lines are stored in `w.keep_list`, while the weak lines are sotred in `w.toss_list`.
+
 ```py
-w = pymoog.weedout.weedout(5000, 4.0, 0, 10830-15, 10830+15, kappa_ratio=0.2, line_list='vald_3000_11000',)
+w = pymoog.weedout.weedout(5000, 2, 0, 10800, 10830, kappa_ratio=0.2)
 w.prepare_file()
 w.run_moog()
+w.read_linelist(remove=False) # remove=False is used for w.compare(); see below.
+```
+
+The difference between the line lists can be seen by:
+
+```py
 w.compare(50000)
-plt.plot(w.wav_all, w.flux_all, label='before weedout')
-plt.plot(w.wav_keep, w.flux_keep, label='after weedout')
+
+plt.figure(figsize=(12, 4), dpi=200)
+ln1 = plt.plot(w.wav_all, w.flux_all, label='Before weedout')
+ln2 = plt.plot(w.wav_keep, w.flux_keep, label='After weedout')
+
+plt.xlabel('Wavelength ($\mathrm{\AA}$)')
+plt.ylabel('Normalized flux (solid)')
+
+plt.twinx()
+ln3 = plt.plot(w.wav_keep, w.flux_keep - w.flux_all, ls='--', c='C3', label='Flux difference')
+plt.ylim(top=0.1)
+plt.ylabel('Flux difference (dashed)')
+
+lns = ln1 + ln2 + ln3
+labs = [l.get_label() for l in lns]
+plt.legend(lns, labs, loc=4)
 ```
 
 ![](../img/driver_guide/weedout.png)

diff --git a/docs/img/driver_guide/binary.png b/docs/img/driver_guide/binary.png
diff --git a/docs/img/driver_guide/cog.png b/docs/img/driver_guide/cog.png
diff --git a/docs/img/driver_guide/weedout.png b/docs/img/driver_guide/weedout.png