fixed some documentation, changed constructor

docs/algorithms/Adjusted.md

 Geomagnetic Adjusted Data
 ===========================================================
 
-Abram Claycomb <[aclaycomb@usgs.gov](mailto:aclaycomb@usgs.gov)>
+Abram Claycomb
+<[aclaycomb@usgs.gov](mailto:aclaycomb@usgs.gov)>
 
 
 ## Background and Motivation
@@ -13,14 +14,23 @@ magnetic field.  The three axes are:
 - `h` - Horizontal 'leading' ahead of the local magnetic
 declination (magnetic north) at the time of installation, so
 that the local magnetic vector would eventually cross the h axis
-- `e` - Horizontal, nominally orthogonal to h (roughly magnetic east)
-- `z` - Nominally vertical, downward, and nominally orthogonal to both `h` and `e`. Vertical at installation on a balancing device with the intended purpose of staying level if the pier on which it is mounted tilts under the sensor, all enclosed under a glass dome to keep air movements from convecting heat directly to the sensor from the room, or pushing the balanced system
-
-Simultaneously, the field is measured by an Overhauser-effect scalar magnetometer (non-directional).  This is called the total field:
+- `e` - Horizontal, nominally orthogonal to h (roughly magnetic
+  east)
+- `z` - Nominally vertical, downward, and nominally orthogonal
+to both `h` and `e`. Vertical at installation on a balancing
+device with the intended purpose of staying level if the pier on
+which it is mounted tilts under the sensor, all enclosed under a
+glass dome to keep air movements from convecting heat directly
+to the sensor from the room, or pushing the balanced system
+
+Simultaneously, the field is measured by an Overhauser-effect
+scalar magnetometer (non-directional).  This is called the total
+field:
 
 - `F` - Total field at the Overhauser pier
 
-A third magnetometer, called a declination-inclination magnetometer (DIM) is used to manually find direction of
+A third magnetometer, called a declination-inclination
+magnetometer (DIM) is used to manually find direction of
 the field for the purpose of calibrating the three-axis sensor
 mentioned above, and converting the coordinate system to that of
 a geographic north, east, and downward set of axes:
@@ -31,8 +41,9 @@ the time of installation, and periodically on a time scale of a
 few years
 - `Y` - Geographically East component of the magnetic field,
 again based on the survey mentioned in `X` above
-- `Z` - Vertical component of the magnetic field, based on
-leveling the theodolite at each absolute measurement session
+- `Z` - Vertical component of the magnetic field, downward,
+ based on leveling the theodolite at each absolute measurement
+ session
 
 The declination and inclination measured by the DIM are:
 
@@ -47,18 +58,23 @@ in the sensor and its alignment to the optical axis of the
 theodolite to which it is mounted.
 
 The real-time measurements (to the nearest second) of `h`, `e`,
-`z` and `F` are used to compute what are known as baselines, or the differences in the pseudo-vector cylindrical coordinate representation.  The equations relating these quantities, with some definitions, are found below:
+`z` and `F` are used to compute what are known as baselines, or
+the differences in the pseudo-vector cylindrical coordinate
+representation.  The equations relating these quantities, with
+some definitions, are found below:
 
 - `F_pier_correction` - measured on the order of once or twice
-per year, by a second Overhauser recording for a few hours at the absolute pier location (in place of the absolute DIM theodolite)
+per year, by a second Overhauser recording for a few hours at
+the absolute pier location (in place of the absolute DIM
+  theodolite)
 - `F_corrected = F + F_pier_correction`
 - `X = F_corrected*cos(I)*cos(D)`
 - `Y = F_corrected*cos(I)*sin(D)`
 - `Z = F_corrected*sin(I)`
-- `H_absolute = X**2 + Y**2 = F_corrected*cos(I)`
+- `H_absolute = sqrt(X**2 + Y**2) = F_corrected*cos(I)`
 - `D_absolute = arctan2(Y,X) = D`
 - `Z_absolute = F_corrected*sin(I)`
-- `H_ordinate = h**2 + e**2` - were the angles small, this may
+- `H_ordinate = sqrt(h**2 + e**2)` - were the angles small, this may
 have been historically approximated as `h`
 - `D_ordinate = arctan2(e,h)` - were the angles small, this may
 have been historically approximated as `e/h`
@@ -74,14 +90,26 @@ account for errors in the vector magnetometer, and transform
 the recorded `h`, `e`, `z` data into `X`, `Y`, `Z` coordinates.
 There are several types of errors:
 
-- non-orthogonal sensor error, which can be corrected by a transformation matrix as a linear operator
-- scale error (measurement by one unit in one sensor not being equal to one unit of the field), which can again be corrected by a different kind of transformation matrix; for fluxgate (and DIM) magnetic sensors, this is known to be temperature-dependent
-- offset error (measurement with no field applied gives a non-zero sensor output; can be corrected by adding a vector, which can be re-cast as a matrix transformation and linear operator by an affine transformation; for fluxgate (and DIM) magnetic sensors, this is known to be temperature-dependent
-- local magnetic disturbances - usually minimized by site selection and disciplined operations during maintenance and measurement.
+- non-orthogonal sensor error, which can be corrected by a
+transformation matrix as a linear operator
+- scale error: measurement by one unit in one sensor not being
+   equal to one unit of the field, which can again be corrected
+   by a different kind of transformation matrix; for fluxgate
+   (and DIM) magnetic sensors, this is known to be
+   temperature-dependent
+- offset error: measurement with no field applied gives a
+  non-zero sensor output; can be corrected by adding a vector,
+  which can be re-cast as a matrix transformation and linear
+  operator by an affine transformation; for fluxgate (and DIM)
+  magnetic sensors, this is known to be temperature-dependent
+- local magnetic disturbances - usually minimized by site
+selection and disciplined operations during maintenance and
+measurement.
 
 The combined effect for the above mentioned errors, as well as
 a final rotation to transform coordinates to X,Y,Z can be found
-using a least-squares algorithm and baseline calculator data.  This is phase one of the Adjusted Data project.
+using a least-squares algorithm and baseline calculator data.  
+This is phase one of the Adjusted Data project.
 
 
 ## Example
@@ -91,7 +119,9 @@ Usage for this algorithm is shown in this
 example.
 
 Example calculations of affine transformation matrices for USGS
-observatories are shown in this [Adjusted Example](AdjustedPhaseOneFunction2.ipynb) IPython notebook.
+observatories are shown in this
+[Adjusted Example](AdjustedPhaseOneFunction2.ipynb) IPython
+notebook.
 
 
 ## References
@@ -100,5 +130,3 @@ observatories are shown in this [Adjusted Example](AdjustedPhaseOneFunction2.ipy
    Int. J. of Forecasting, 19(1), 143-148.
 
  - Hitchman, P. G., Crosthwaite, W. V., Lewis, A. M., and Wang, L. (2011), [Australian Geomagnetism Report 2011](https://d28rz98at9flks.cloudfront.net/73627/Rec2012_072.pdf)
-
- 

docs/algorithms/Adjusted_usage.md

 Adjusted Algorithm Usage
 ========================
 
-The Adjusted Algorithm transforms between `observatory`, and `geographic`,
-channel orientations, using transform matrices derived from absolute and
-baseline measurements.  Read more about the [Adjusted Algorithm](./Adjusted.md).
+The Adjusted Algorithm transforms between `observatory`, and
+`geographic`, channel orientations, using transform matrices
+derived from absolute and baseline measurements.  Read more about
+the [Adjusted Algorithm](./Adjusted.md).
 
 `geomag.py --algorithm sqdist`
 
 ### Example
 
 This example uses a state file to produce X, Y, Z and F channels
-from raw H, E, Z and F channels using the EDGE channel naming convention.  Absolutes were used to compute a transform matrix contained in the statefile.  The pier correction is also currently contained in the statefile.
+from raw H, E, Z and F channels using the EDGE channel naming
+convention.  Absolutes were used to compute a transform matrix
+contained in the statefile.  The pier correction is also currently
+contained in the statefile.
 
     bin/geomag.py \
       --input-edge cwbpub.cr.usgs.gov \
       --observatory BOU \
       --inchannels H E Z F \
-      --starttime 2016-01-03T00:01:00 \
-      --endtime 2016-01-04T00:00:00 \
+      --starttime 2016-01-03T00:00:00 \
+      --endtime 2016-01-03T23:59:59 \
       --algorithm adjusted \
-      --adjusted-statefile=/tmp/adjbou_state_.json \
+      --adjusted-statefile=/etc/adjusted/adjbou_state_.json \
       --outchannels X Y Z F \
       --output-iaga-stdout
 
 
 ### Library Notes
 
-> Note: this library internally represents data gaps as NaN, and factories
+> Note: this library internally represents data gaps as NaN, and
+factories
 > convert to this where possible.

docs/api.md

@@ -47,9 +47,9 @@ Exception base class is `geomagio.TimeseriesFactoryException`.
 Base class is `geomagio.algorithm.Algorithm`
 Exception base class is `geomagio.algorithm.AlgorithmException`
 
+- Adjusted `geomagio.algorithm.AdjustedAlgorithm`
 - Delta F `geomagio.algorithm.DeltaFAlgorithm`
 - XYZ `geomagio.algorithm.XYZAlgorithm`
-- Adjusted `geomagio.algorithm.AdjustedAlgorithm`
 
 
 ## Example

docs/usage.md

@@ -71,6 +71,14 @@ data to an **_iaga2002_** formatted file:
 
 There are flags to specify certain algorithms should be run against the data.
 
+### Adjusted ###
+
+`--algorithm adjusted`
+
+`--adjusted-statefile=/etc/adjusted/adjbou_state_.json`
+
+`--outchannels X Y Z F `
+
 #### XYZ ####
 
 `--algorithm xyz`
@@ -85,7 +93,7 @@ Rotate data from HEZ (obs) or HDZ (mag) to XYZ (geo) and back.
 
 Document: [/algorithms/XYZ_usage.md](./algorithms/XYZ_usage.md)
 
-### Adjusted ###
+
 
 
 

geomagio/algorithm/AdjustedAlgorithm.py

@@ -19,7 +19,9 @@ class AdjustedAlgorithm(Algorithm):
         self.matrix = matrix
         self.pier_correction = pier_correction
         self.statefile = statefile
-        self.load_state()
+        if (matrix is None):
+            self.load_state()
+
 
     def load_state(self):
         """Load algorithm state from a file.
@@ -107,9 +109,9 @@ class AdjustedAlgorithm(Algorithm):
         stats = Stats(stats)
         stats.data_type = 'adjusted'
         stats.location = 'A0'
-        Trace = super(AdjustedAlgorithm, cls).create_trace(channel, stats,
+        trace = super(AdjustedAlgorithm, cls).create_trace(channel, stats,
             data)
-        return Trace
+        return trace
 
     def process(self, stream):
         """Run algorithm for a stream.

geomagio/algorithm/__init__.py

@@ -6,18 +6,19 @@ Geomag Algorithms module
 from Algorithm import Algorithm
 from AlgorithmException import AlgorithmException
 # algorithms
+from AdjustedAlgorithm import AdjustedAlgorithm
 from DeltaFAlgorithm import DeltaFAlgorithm
 from SqDistAlgorithm import SqDistAlgorithm
 from XYZAlgorithm import XYZAlgorithm
-from AdjustedAlgorithm import AdjustedAlgorithm
+
 
 # algorithms is used by Controller to auto generate arguments
 algorithms = {
     'identity': Algorithm,
+    'adjusted': AdjustedAlgorithm,
     'deltaf': DeltaFAlgorithm,
     'sqdist': SqDistAlgorithm,
-    'xyz': XYZAlgorithm,
-    'adjusted': AdjustedAlgorithm
+    'xyz': XYZAlgorithm
 }
 
 
@@ -26,8 +27,8 @@ __all__ = [
     'Algorithm',
     'AlgorithmException',
     # algorithms
+    'AdjustedAlgorithm',
     'DeltaFAlgorithm',
     'SqDistAlgorithm',
     'XYZAlgorithm'
-    'AdjustedAlgorithm'
 ]