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Commit c7eaf01e authored by Russell, Hannah's avatar Russell, Hannah
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update elbe ipynb files and names

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ipynb/Elbe_Chlorophyll.ipynb 0 → 100644
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View file @ c7eaf01e
%% Cell type:code id:3d380a50 tags:
``` python
import glob
import os
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
```
%% Cell type:markdown id:3c79ca53 tags:
## pre-processing elbe Chlorophyll data
The general aim is to create concateable (non-2d i guess) data frames of all estuaries with unified column names
%% Cell type:code id:bdd39076 tags:
``` python
#os.getcwd()
os.chdir("C:\\Users\\Hannah Russell\\north_sea_estuaries_visualisations")
cwd = os.path.abspath(os.curdir)
elbe_clorophyll_df_1 = glob.glob(os.path.join(cwd, 'data', 'input', 'elbe', 'chlorophyll','df_1', '*.csv'))
elbe_clorophyll_df_1 = [pd.read_csv(file, sep = ';', encoding= 'unicode_escape') for file in elbe_clorophyll_df_1]
elbe_clorophyll_df_1 = pd.concat(elbe_clorophyll_df_1, ignore_index=True)
#elbe_clorophyll_df_1.head()
```
%% Cell type:code id:c68f4427 tags:
``` python
elbe_clorophyll_df_1.columns = elbe_clorophyll_df_1.columns.str.replace("['']", "")
elbe_clorophyll_df_1.drop(elbe_clorophyll_df_1[elbe_clorophyll_df_1.Messwert.str.contains('[<]', na=True)].index, inplace=True) # removed < from columns with <2.0 string
elbe_clorophyll_df_1['Stromkilometer'] = elbe_clorophyll_df_1['Stromkilometer'].str.replace(",", ".")
elbe_clorophyll_df_1['Messwert'] = elbe_clorophyll_df_1['Messwert'].str.replace(",", ".")
#elbe_clorophyll_df_1.head()
```
%% Output
C:\Users\HANNAH~1\AppData\Local\Temp/ipykernel_18444/3904582180.py:1: FutureWarning: The default value of regex will change from True to False in a future version.
elbe_clorophyll_df_1.columns = elbe_clorophyll_df_1.columns.str.replace("['']", "")
%% Cell type:code id:f98cec41 tags:
``` python
Stromkilometer = elbe_clorophyll_df_1['Stromkilometer'].astype(float)
Messwert = elbe_clorophyll_df_1['Messwert'].astype(float)
# plot of all cholorphyll values from all years on one plot
plt.scatter(Stromkilometer, Messwert)
plt.gca().invert_xaxis()
plt.title('Elbe-- All Years')
plt.xlabel('Kilometer')
plt.ylabel('Chlorophyll ug/L')
```
%% Output
Text(0, 0.5, 'Chlorophyll ug/L')
%% Cell type:code id:6b548829 tags:
``` python
elbe_chlor_df_1_med = elbe_clorophyll_df_1[['Stromkilometer', 'Messwert']]
elbe_chlor_df_1_med.dropna()
elbe_chlor_df_1_med = elbe_chlor_df_1_med.groupby('Stromkilometer', as_index=False).median()
stromkilometer_med = elbe_chlor_df_1_med['Stromkilometer']
messwert_med = elbe_chlor_df_1_med['Messwert']
#elbe_chlor_df_1_med.head()
```
%% Cell type:code id:8ebebf61 tags:
``` python
# Chlorophyll values from all years
plt.plot(stromkilometer_med, messwert_med)
plt.gca().invert_xaxis()
plt.title('Elbe-- Median at km')
plt.xlabel('Kilometer')
plt.ylabel('Chlorophyll ug/L')
```
%% Output
Text(0, 0.5, 'Chlorophyll ug/L')
%% Cell type:markdown id:0e70af95 tags:
## elbe depth
%% Cell type:code id:b7f50efe tags:
``` python
elbe_depth_df_1 = pd.read_csv(cwd + "/data/input/elbe/depth/df_1/Schelde Depth.csv")
elbe_depth_df_1['Stromkilometer'] = elbe_depth_df_1['Stromkilometer'].astype(float).round(1)
Stromkilometer_d = elbe_depth_df_1['Stromkilometer']
Depth = elbe_depth_df_1['Depth']
elbe_depth_df_1
# Depth plot
plt.plot(Stromkilometer_d, Depth)
plt.gca().invert_xaxis()
plt.gca().invert_yaxis()
plt.title('Elbe-- All Years')
plt.xlabel('Kilometer')
plt.ylabel('Depth')
```
%% Output
Text(0, 0.5, 'Depth')
%% Cell type:markdown id:d37aec35 tags:
## Elbe dephth and chlorophyll
%% Cell type:code id:02479b31 tags:
``` python
# create figure and axis objects with subplots()
fig,ax1 = plt.subplots()
ax2 = ax1.twinx()
ax1.plot(stromkilometer_med, messwert_med, color="red") # this line won't show up when there is a limit on the x axis
ax2.plot(Stromkilometer_d, Depth, color="blue")
# x-axis
ax1.set_xlabel("Stromkilometer", fontsize = 14)
ax2.set_xlim(586,830) # red line is apparently outside these limits even though the data is in that range
plt.xticks(np.arange(550, 850, step=50))
plt.gca().invert_xaxis()
# y-axes
ax1.set_ylabel("Messwert", color="red", fontsize=14)
ax2.set_ylabel("Depth",color="blue",fontsize=14)
ax2.invert_yaxis()
```
%% Output
%% Cell type:code id:242cf914 tags:
``` python
```
ipynb/Elbe_Turbidity.ipynb 0 → 100644
+ 659
− 0
View file @ c7eaf01e
%% Cell type:code id:f6efd717 tags:
``` python
import glob
import os
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
```
%% Cell type:markdown id:801e0dd2 tags:
## pre-processing elbe Chlorophyll data
%% Cell type:code id:9188cca4 tags:
``` python
# Get xls files list from a folder
#os.getcwd()
os.chdir("C:\\Users\\Hannah Russell\\north_sea_estuaries_visualisations")
cwd = os.path.abspath(os.curdir)
elbe_turbidity_df_1 = glob.glob(os.path.join(cwd, 'data', 'input', 'elbe', 'turbidity','df_1', '*.xls'))
elbe_turbidity_df_1 = [pd.read_excel(file) for file in elbe_turbidity_df_1]
#df_list = (pd.read_excel(file) for file in xls_files)
elbe_turbidity_df_1 = pd.concat(elbe_turbidity_df_1, ignore_index=True)
elbe_turbidity_df_1.head()
```
%% Output
Gew�sser Wasserk�rper Messstelle Stromkilometer \
0 Elbe Elbe-West Blankenese (Strom-km 634,3) 634.3
1 Elbe Elbe-West Blankenese (Strom-km 634,3) 634.3
2 Elbe Elbe-West Blankenese (Strom-km 634,3) 634.3
3 Elbe Elbe-West Blankenese (Strom-km 634,3) 634.3
4 Elbe Elbe-West Blankenese (Strom-km 634,3) 634.3
Parameter Messwert Einheit Messwerttyp \
0 Trübung (FNU) 30,6 FNU quantitativ nachgewiesen
1 Trübung (FNU) 39,7 FNU quantitativ nachgewiesen
2 Trübung (FNU) 37,2 FNU quantitativ nachgewiesen
3 Trübung (FNU) 34,0 FNU quantitativ nachgewiesen
4 Trübung (FNU) 35,1 FNU quantitativ nachgewiesen
Medium Messwertart Messvorgang \
0 Wasser - Gesamtprobe Tagesmittelwert kontinuierliche Messungen
1 Wasser - Gesamtprobe Tagesmittelwert kontinuierliche Messungen
2 Wasser - Gesamtprobe Tagesmittelwert kontinuierliche Messungen
3 Wasser - Gesamtprobe Tagesmittelwert kontinuierliche Messungen
4 Wasser - Gesamtprobe Tagesmittelwert kontinuierliche Messungen
Datum Bezugsjahr Zeit Datum bis Zeit bis Status \
0 02.01.1997 1997 NaN NaN NaN freigegeben
1 03.01.1997 1997 NaN NaN NaN freigegeben
2 06.01.1997 1997 NaN NaN NaN freigegeben
3 07.01.1997 1997 NaN NaN NaN freigegeben
4 08.01.1997 1997 NaN NaN NaN freigegeben
Analysemethode Bemerkung (Datenausgabe) zus�tzliche Informationen
0 - NaN NaN
1 - NaN NaN
2 - NaN NaN
3 - NaN NaN
4 - NaN NaN
%% Cell type:code id:094afe71 tags:
``` python
elbe_turbidity_df_1['Messwert'] = elbe_turbidity_df_1['Messwert'].str.replace(",", ".")
elbe_turbidity_df_1.drop(elbe_turbidity_df_1[elbe_turbidity_df_1.Stromkilometer.str.contains('[Nebenge]', na=False)].index, inplace=True)
Stromkilometer = elbe_turbidity_df_1['Stromkilometer'].astype(float)
Messwert = elbe_turbidity_df_1['Messwert'].astype(float)
```
%% Cell type:code id:bb4beeaa tags:
``` python
#plot all values on one plot
plt.scatter(Stromkilometer, Messwert)
plt.gca().invert_xaxis()
plt.xlim(586,700) #Geestacht is at ~586 km
plt.title('Elbe-- All Years')
plt.xlabel('Kilometer')
plt.ylabel('Turbidity FNU')
```
%% Output
Text(0, 0.5, 'Turbidity FNU')
%% Cell type:code id:b638e47d tags:
``` python
turb_avg = turbidity[['Stromkilometer', 'Messwert']]
turb_avg.dropna()
turb_avg = turb_avg.groupby('Stromkilometer', as_index = False).median() #for some reason this is invalid even though median() works... not sure yet what's wrong here
turb_avg
```
%% Output
Stromkilometer Messwert
0 3.9 10.5
1 26.5 3.8
2 89.6 11.7
3 172.6 14.6
4 216.6 13.4
5 318.1 20.0
6 470.0 10.9
7 474.5 19.5
8 609.8 18.2
9 628.9 30.6
10 634.3 25.6
11 660.6 73.8
%% Cell type:code id:c2739d4d tags:
``` python
km_avg = turb_avg['Stromkilometer']
Messwert_avg = turb_avg['Messwert']
plt.plot(km_avg, Messwert_avg)
plt.gca().invert_xaxis()
plt.title('Elbe-- Median at km')
plt.xlabel('Kilometer')
plt.ylabel('turbidity')
```
%% Output
Text(0, 0.5, 'turbidity')
%% Cell type:code id:f84bdb72 tags:
``` python
elbe_depth = pd.read_csv('Elbe Depth.csv')
elbe_depth['Stromkilometer'] = elbe_depth['Stromkilometer'].astype(float).round(1)
Stromkilometer2 = elbe_depth['Stromkilometer']
Depth = elbe_depth['Depth']
elbe_depth
```
%% Output
Stromkilometer Depth
0 537.9 -2.574074
1 546.2 -1.666667
2 561.8 0.131687
3 572.3 0.370370
4 579.6 1.267490
.. ... ...
131 821.8 25.481481
132 823.2 26.518519
133 824.9 24.888889
134 826.0 24.444444
135 828.8 25.481481
[136 rows x 2 columns]
%% Cell type:code id:2da93d63 tags:
``` python
# create figure and axis objects with subplots()
fig,ax1 = plt.subplots()
ax2 = ax1.twinx()
# make a plot
ax1.plot(km_avg, Messwert_avg, color="red") # this line won't show up when there is a limit on the x axis
ax2.plot(Stromkilometer2, Depth, color="blue")
# x-axis
ax1.set_xlabel("Stromkilometer", fontsize = 14)
ax2.set_xlim(586,830)
plt.xticks(np.arange(550, 850, step=50))
plt.gca().invert_xaxis()
# y-axis labels
ax1.set_ylabel("Messwert", color="red", fontsize=14)
ax2.set_ylabel("Depth",color="blue",fontsize=14)
ax2.invert_yaxis()
```
%% Output
%% Cell type:code id:81a50a6c tags:
``` python
```
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